Nucleic acids and proteins from Streptococcus groups A & B

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a National Stage application of co-pending PCT application PCT/GB01/04789 filed Oct. 29, 2001, which was published in English under PCT Article 21(2) on May 2, 2002, which claims the benefit of Great Britain applications Serial No. GB0026333.5 filed Oct. 27, 2000, Serial No. GB0028727.6 filed Nov. 24, 2000, and Serial No. GB0105640.7 filed Mar. 7, 2001. These applications are incorporated herein by reference in their entireties.

REFERENCE TO A “SEQUENCE LISTING”

This application incorporates by reference a 21.0 MB text file created on Nov. 27, 2009 and labeled “10415182_sequence_listing.txt,” which is the listing for this application.

All documents cited herein are incorporated by reference in their entirety.

TECHNICAL FIELD

This invention relates to nucleic acid and proteins from the bacteria <i>Streptococcus agalactiae </i>(GBS) and <i>Streptococcus pyogenes </i>(GAS).

BACKGROUND ART

Once thought to infect only cows, the Gram-positive bacterium <i>Streptococcus agalactiae </i>(or “group B <i>streptococcus</i>”, abbreviated to “GBS”) is now known to cause serious disease, bacteremia and meningitis, in immunocompromised individuals and in neonates. There are two types of neonatal infection. The first (early onset, usually within 5 days of birth) is manifested by bacteremia and pneumonia. It is contracted vertically as a baby passes through the birth canal. GBS colonises the vagina of about 25% of young women, and approximately 1% of infants born via a vaginal birth to colonised mothers will become infected. Mortality is between 50-70%. The second is a meningitis that occurs 10 to 60 days after birth. If pregnant women are vaccinated with type III capsule so that the infants are passively immunised, the incidence of the late onset meningitis is reduced but is not entirely eliminated.

The “B” in “GBS” refers to the Lancefield classification, which is based on the antigenicity of a carbohydrate which is soluble in dilute acid and called the C carbohydrate. Lancefield identified 13 types of C carbohydrate, designated A to O, that could be serologically differentiated. The organisms that most commonly infect humans are found in groups A, B, D, and G. Within group B, strains can be divided into 8 serotypes (Ia, Ib, Ia/c, II, III, IV, V, and VI) based on the structure of their polysaccharide capsule.

Group A <i>streptococcus </i>(“GAS”, <i>S. pyogenes</i>) is a frequent human pathogen, estimated to be present in between 5-15% of normal individuals without signs of disease. When host defenses are compromised, or when the organism is able to exert its virulence, or when it is introduced to vulnerable tissues or hosts, however, an acute infection occurs. Diseases include puerperal fever, scarlet fever, erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis and streptococcal toxic shock syndrome.

<i>S. pyogenes </i>is typically treated using antibiotics. Although <i>S. agalactiae </i>is inhibited by antibiotics, however, it is not killed by penicillin as easily as GAS. Prophylactic vaccination is thus preferable.

Current GBS vaccines are based on polysaccharide antigens, although these suffer from poor immunogenicity. Anti-idiotypic approaches have also been used (e.g. WO99/54457). There remains a need, however, for effective adult vaccines against <i>S. agalactiae </i>infection. There also remains a need for vaccines against <i>S. pyogenes </i>infection.

It is an object of the invention to provide proteins which can be used in the development of such vaccines. The proteins may also be useful for diagnostic purposes, and as targets for antibiotics.

DISCLOSURE OF THE INVENTION

The invention provides proteins comprising the <i>S. agalactiae </i>amino acid sequences disclosed in the examples, and proteins comprising the <i>S. pyogenes </i>amino acid sequences disclosed in the examples. These amino acid sequences are the even SEQ IDs between 1 and 10960.

It also provides proteins comprising amino acid sequences having sequence identity to the <i>S. agalactiae </i>amino acid sequences disclosed in the examples, and proteins comprising amino acid sequences having sequence identity to the <i>S. pyogenes </i>amino acid sequences disclosed in the examples. Depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g. 60%, 70%, 80%, 90%, 95%, 99% or more). These proteins include homologs, orthologs, allelic variants and functional mutants. Typically, 50% identity or more between two proteins is considered to be an indication of functional equivalence. Identity between proteins is preferably determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty=12 and gap extension penalty=1.

Preferred proteins of the invention are GBS1 to GBS689 (see Table IV).

The invention further provides proteins comprising fragments of the <i>S. agalactiae </i>amino acid sequences disclosed in the examples, and proteins comprising fragments of the <i>S. pyogenes </i>amino acid sequences disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the sequences and, depending on the particular sequence, n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more). Preferably the fragments comprise one or more epitopes from the sequence. Other preferred fragments are (a) the N-terminal signal peptides of the proteins disclosed in the examples, (b) the proteins disclosed in the examples, but without their N-terminal signal peptides, (c) fragments common to the related GAS and GBS proteins disclosed in the examples, and (d) the proteins disclosed in the examples, but without their N-terminal amino acid residue.

The proteins of the invention can, of course, be prepared by various means (e.g. recombinant expression, purification from GAS or GBS, chemical synthesis etc.) and in various forms (e.g. native, fusions, glycosylated, non-glycosylated etc.). They are preferably prepared in substantially pure form (i.e. substantially free from other streptococcal or host cell proteins) or substantially isolated form. Proteins of the invention are preferably streptococcal proteins.

According to a further aspect, the invention provides antibodies which bind to these proteins. These may be polyclonal or monoclonal and may be produced by any suitable means (e.g. by recombinant expression). To increase compatibility with the human immune system, the antibodies may be chimeric or humanised (e.g. Breedveld (2000) <i>Lancet </i>355(9205):735-740; Gorman &amp; Clark (1990) <i>Semin. Immunol. </i>2:457-466), or fully human antibodies may be used. The antibodies may include a detectable label (e.g. for diagnostic assays).

According to a further aspect, the invention provides nucleic acid comprising the <i>S. agalactiae </i>nucleotide sequences disclosed in the examples, and nucleic acid comprising the <i>S. pyogenes </i>nucleotide sequences disclosed in the examples. These nucleic acid sequences are the odd SEQ IDs between 1 and 10966.

In addition, the invention provides nucleic acid comprising nucleotide sequences having sequence identity to the <i>S. agalactiae </i>nucleotide sequences disclosed in the examples, and nucleic acid comprising nucleotide sequences having sequence identity to the <i>S. pyogenes </i>nucleotide sequences disclosed in the examples. Identity between sequences is preferably determined by the Smith-Waterman homology search algorithm as described above.

Furthermore, the invention provides nucleic acid which can hybridise to the <i>S. agalactiae </i>nucleic acid disclosed in the examples, and nucleic acid which can hybridise to the <i>S. pyogenes </i>nucleic acid disclosed in the examples preferably under ‘high stringency’ conditions (e.g. 65° C. in 0.1×SSC, 0.5% SDS solution).

Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least n consecutive nucleotides from the <i>S. agalactiae </i>or <i>S. pyogenes </i>sequences and, depending on the particular sequence, n is 10 or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200 or more). The fragments may comprise sequences which are common to the related GAS and GBS sequences disclosed in the examples.

According to a further aspect, the invention provides nucleic acid encoding the proteins and protein fragments of the invention.

The invention also provides: nucleic acid comprising nucleotide sequence SEQ ID 10967; nucleic acid comprising nucleotide sequences having sequence identity to SEQ ID 10967; nucleic acid which can hybridise to SEQ ID 10967 (preferably under ‘high stringency’ conditions); nucleic acid comprising a fragment of at least n consecutive nucleotides from SEQ ID 10967, wherein n is 10 or more e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1500, 2000, 3000, 4000, 5000, 10000, 100000, 1000000 or more Nucleic acids of the invention can be used in hybridisation reactions (e.g. Northern or Southern blots, or in nucleic acid microarrays or ‘gene chips’) and amplification reactions (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA etc.) and other nucleic acid techniques.

It should also be appreciated that the invention provides nucleic acid comprising sequences complementary to those described above (e.g. for antisense or probing, or for use as primers).

Nucleic acid according to the invention can, of course, be prepared in many ways (e.g. by chemical synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various forms (e.g. single stranded, double stranded, vectors, primers, probes, labelled etc.). The nucleic acid is preferably in substantially isolated form.

Nucleic acid according to the invention may be labelled e.g. with a radioactive or fluorescent label. This is particularly useful where the nucleic acid is to be used in nucleic acid detection techniques e.g. where the nucleic acid is a primer or as a probe for use in techniques such as PCR, LCR, TMA, NASBA etc.

In addition, the term “nucleic acid” includes DNA and RNA, and also their analogues, such as those containing modified backbones, and also peptide nucleic acids (PNA) etc.

According to a further aspect, the invention provides vectors comprising nucleotide sequences of the invention (e.g. cloning or expression vectors) and host cells transformed with such vectors.

According to a further aspect, the invention provides compositions comprising protein, antibody, and/or nucleic acid according to the invention. These compositions may be suitable as immunogenic compositions, for instance, or as diagnostic reagents, or as vaccines.

The invention also provides nucleic acid, protein, or antibody according to the invention for use as medicaments (e.g. as immunogenic compositions or as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid, protein, or antibody according to the invention in the manufacture of: (i) a medicament for treating or preventing disease and/or infection caused by <i>streptococcus</i>; (ii) a diagnostic reagent for detecting the presence of <i>streptococcus </i>or of antibodies raised against <i>streptococcus</i>; and/or (iii) a reagent which can raise antibodies against <i>streptococcus</i>. Said <i>streptococcus </i>may be any species, group or strain, but is preferably <i>S. agalactiae</i>, especially serotype III or V, or <i>S. pyogenes</i>. Said disease may be bacteremia, meningitis, puerperal fever, scarlet fever, erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis or toxic shock syndrome.

The invention also provides a method of treating a patient, comprising administering to the patient a therapeutically effective amount of nucleic acid, protein, and/or antibody of the invention. The patient may either be at risk from the disease themselves or may be a pregnant woman (‘maternal immunisation’ e.g. Glezen &amp; Alpers (1999) <i>Clin. Infect. Dis. </i>28:219-224).

Administration of protein antigens is a preferred method of treatment for inducing immunity.

Administration of antibodies of the invention is another preferred method of treatment. This method of passive immunisation is particularly useful for newborn children or for pregnant women. This method will typically use monoclonal antibodies, which will be humanised or fully human.

The invention also provides a kit comprising primers (e.g. PCR primers) for amplifying a template sequence contained within a <i>Streptococcus </i>(e.g. <i>S. pyogenes </i>or <i>S. agalactiae</i>) nucleic acid sequence, the kit comprising a first primer and a second primer, wherein the first primer is substantially complementary to said template sequence and the second primer is substantially complementary to a complement of said template sequence, wherein the parts of said primers which have substantial complementarity define the termini of the template sequence to be amplified. The first primer and/or the second primer may include a detectable label (e.g. a fluorescent label).

The invention also provides a kit comprising first and second single-stranded oligonucleotides which allow amplification of a <i>Streptococcus </i>template nucleic acid sequence contained in a single- or double-stranded nucleic acid (or mixture thereof), wherein: (a) the first oligonucleotide comprises a primer sequence which is substantially complementary to said template nucleic acid sequence; (b) the second oligonucleotide comprises a primer sequence which is substantially complementary to the complement of said template nucleic acid sequence; (c) the first oligonucleotide and/or the second oligonucleotide comprise(s) sequence which is not complementary to said template nucleic acid; and (d) said primer sequences define the termini of the template sequence to be amplified. The non-complementary sequence(s) of feature (c) are preferably upstream of (i.e. 5′ to) the primer sequences. One or both of these (c) sequences may comprise a restriction site (e.g. EP-B-0509612) or a promoter sequence (e.g. EP-B-0505012). The first oligonucleotide and/or the second oligonucleotide may include a detectable label (e.g. a fluorescent label).

The template sequence may be any part of a genome sequence (e.g. SEQ ID 10967). For example, it could be a rRNA gene (e.g. Turenne et al. (2000) <i>J. Clin. Microbiol. </i>38:513-520; SEQ IDs 12018-12024 herein) or a protein-coding gene. The template sequence is preferably specific to GBS.

The invention also provides a computer-readable medium (e.g. a floppy disk, a hard disk, a CD-ROM, a DVD etc.) and/or a computer database containing one or more of the sequences in the sequence listing. The medium preferably contains SEQ ID 10967.

The invention also provides a hybrid protein represented by the formula NH₂-A-[-X-L-]_n-B—COOH, wherein X is a protein of the invention, L is an optional linker amino acid sequence, A is an optional N-terminal amino acid sequence, B is an optional C-terminal amino acid sequence, and n is an integer greater than 1. The value of n is between 2 and x, and the value of x is typically 3, 4, 5, 6, 7, 8, 9 or 10. Preferably n is 2, 3 or 4; it is more preferably 2 or 3; most preferably, n=2. For each n instances, —X— may be the same or different. For each n instances of [-X-L-], linker amino acid sequence -L- may be present or absent. For instance, when n=2 the hybrid may be NH₂—X₁-L₁-X₂-L₂-COOH, NH₂—X₁-X₂—COOH, NH₂—X₁-L₁-X₂—COOH, NH₂—X₁-X₂-L₂-COOH, etc. Linker amino acid sequence(s) -L- will typically be short (e.g. 20 or fewer amino acids i.e. 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. Gly_nwhere n=2, 3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. His_nwhere n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art. -A- and —B— are optional sequences which will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct protein trafficking, or short peptide sequences which facilitate cloning or purification (e.g. histidine tags i.e. His_nwhere n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable N-terminal and C-terminal amino acid sequences will be apparent to those skilled in the art. In some embodiments, each X will be a GBS sequence; in others, mixtures of GAS and GBS will be used.

According to further aspects, the invention provides various processes.

A process for producing proteins of the invention is provided, comprising the step of culturing a host cell of to the invention under conditions which induce protein expression.

A process for producing protein or nucleic acid of the invention is provided, wherein the protein or nucleic acid is synthesised in part or in whole using chemical means.

A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridising conditions to form duplexes; and (b) detecting said duplexes.

A process for detecting <i>Streptococcus </i>in a biological sample (e.g. blood) is also provided, comprising the step of contacting nucleic acid according to the invention with the biological sample under hybridising conditions. The process may involve nucleic acid amplification (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA etc.) or hybridisation (e.g. microarrays, blots, hybridisation with a probe in solution etc.). PCR detection of <i>Streptococcus </i>in clinical samples, in particular <i>S. pyogenes</i>, has been reported [see e.g. Louie et al. (2000) <i>CMAJ </i>163:301-309; Louie et al. (1998) <i>J. Clin. Microbiol. </i>36:1769-1771]. Clinical assays based on nucleic acid are described in general in Tang et al. (1997) <i>Clin. Chem. </i>43:2021-2038.

A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting an antibody of the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.

A process for identifying an amino acid sequence is provided, comprising the step of searching for putative open reading frames or protein-coding regions within a genome sequence of <i>S. agalactiae</i>. This will typically involve in silico searching the sequence for an initiation codon and for an in-frame termination codon in the downstream sequence. The region between these initiation and termination codons is a putative protein-coding sequence. Typically, all six possible reading frames will be searched. Suitable software for such analysis includes ORFFINDER (NCBI), GENEMARK [Borodovsky &amp; McIninch (1993) <i>Computers Chem. </i>17:122-133), GLIMMER [Salzberg et al. (1998) <i>Nucleic Acids Res. </i>26:544-548; Salzberg et al. (1999) <i>Genomics </i>59:24-31; Delcher et al. (1999) <i>Nucleic Acids Res. </i>27:4636-4641], or other software which uses Markov models [e.g. Shmatkov et al. (1999) <i>Bioinformatics </i>15:874-876]. The invention also provides a protein comprising the identified amino acid sequence. These proteins can then expressed using conventional techniques.

The invention also provides a process for determining whether a test compound binds to a protein of the invention. If a test compound binds to a protein of the invention and this binding inhibits the life cycle of the GBS bacterium, then the test compound can be used as an antibiotic or as a lead compound for the design of antibiotics. The process will typically comprise the steps of contacting a test compound with a protein of the invention, and determining whether the test compound binds to said protein. Preferred proteins of the invention for use in these processes are enzymes (e.g. tRNA synthetases), membrane transporters and ribosomal proteins. Suitable test compounds include proteins, polypeptides, carbohydrates, lipids, nucleic acids (e.g. DNA, RNA, and modified forms thereof), as well as small organic compounds (e.g. MW between 200 and 2000 Da). The test compounds may be provided individually, but will typically be part of a library (e.g. a combinatorial library). Methods for detecting a binding interaction include NMR, filter-binding assays, gel-retardation assays, displacement assays, surface plasmon resonance, reverse two-hybrid etc. A compound which binds to a protein of the invention can be tested for antibiotic activity by contacting the compound with GBS bacteria and then monitoring for inhibition of growth. The invention also provides a compound identified using these methods.

The invention also provides a composition comprising a protein or the invention and one or more of the following antigens: <ul><li id="ul0001-0001" num="0000"><ul><li id="ul0002-0001" num="0047">a protein antigen from <i>Helicobacter pylori </i>such as VacA, CagA, NAP, HopX, HopY [e.g. WO98/04702] and/or urease.</li><li id="ul0002-0002" num="0048">a protein antigen from <i>N. meningitidis </i>serogroup B, such as those in WO99/24578, WO99/36544, WO99/57280, WO00/22430, Tettelin et al. (2000) <i>Science </i>287:1809-1815, Pizza et al. (2000) <i>Science </i>287:1816-1820 and WO96/29412, with protein ‘287’ and derivatives being particularly preferred.</li><li id="ul0002-0003" num="0049">an outer-membrane vesicle (OMV) preparation from <i>N. meningitidis </i>serogroup B, such as those disclosed in WO01/52885; Bjune et al. (1991) <i>Lancet </i>338(8775):1093-1096; Fukasawa et al. (1999) <i>Vaccine </i>17:2951-2958; Rosenqvist et al. (1998) <i>Dev. Biol. Stand. </i>92:323-333 etc.</li><li id="ul0002-0004" num="0050">a saccharide antigen from <i>N. meningitidis </i>serogroup A, C, W135 and/or Y, such as the oligosaccharide disclosed in Costantino et al. (1992) <i>Vaccine </i>10:691-698 from serogroup C [see also Costantino et al. (1999) <i>Vaccine </i>17:1251-1263].</li><li id="ul0002-0005" num="0051">a saccharide antigen from <i>Streptococcus pneumoniae </i>[e.g. Watson (2000) <i>Pediatr Infect Dis J </i>19:331-332; Rubin (2000) <i>Pediatr Clin North Am </i>47:269-285, v; Jedrzejas (2001) <i>Microbiol Mol Biol Rev </i>65:187-207].</li><li id="ul0002-0006" num="0052">an antigen from hepatitis A virus, such as inactivated virus [e.g. Bell (2000) <i>Pediatr Infect Dis J </i>19:1187-1188; Iwarson (1995) <i>APMIS </i>103:321-326].</li><li id="ul0002-0007" num="0053">an antigen from hepatitis B virus, such as the surface and/or core antigens [e.g. Gerlich et al. (1990) <i>Vaccine </i>8 Suppl:S63-68 &amp; 79-80].</li><li id="ul0002-0008" num="0054">an antigen from hepatitis C virus [e.g. Hsu et al. (1999) <i>Clin Liver Dis </i>3:901-915].</li><li id="ul0002-0009" num="0055">an antigen from <i>Bordetella pertussis</i>, such as pertussis holotoxin (PT) and filamentous haemagglutinin (FHA) from <i>B. pertussis</i>, optionally also in combination with pertactin and/or agglutinogens 2 and 3 [e.g. Gustafsson et al. (1996) <i>N. Engl. J. Med. </i>334:349-355; Rappuoli et al. (1991) <i>TIBTECH </i>9:232-238].</li><li id="ul0002-0010" num="0056">a diphtheria antigen, such as a diphtheria toxoid [e.g. chapter 3 of Vaccines (1988) eds. Plotkin &amp; Mortimer. ISBN 0-7216-1946-0] e.g. the CRM₁₉₇mutant [e.g. Del Guidice et al. (1998) <i>Molecular Aspects of Medicine </i>19:1-70].</li><li id="ul0002-0011" num="0057">a tetanus antigen, such as a tetanus toxoid [e.g. chapter 4 of Plotkin &amp; Mortimer].</li><li id="ul0002-0012" num="0058">a saccharide antigen from <i>Haemophilus influenzae </i>B.</li><li id="ul0002-0013" num="0059">an antigen from <i>N. gonorrhoeae </i>[e.g. WO99/24578, WO99/36544, WO99/57280].</li><li id="ul0002-0014" num="0060">an antigen from <i>Chlamydia pneumoniae </i>[e.g. PCT/IB01/01445; Kalman et al. (1999) <i>Nature Genetics </i>21:385-389; Read et al. (2000) <i>Nucleic Acids Res </i>28:1397-406; Shirai et al. (2000) <i>J. Infect. Dis. </i>181(Suppl 3):S524-S527; WO99/27105; WO00/27994; WO00/37494].</li><li id="ul0002-0015" num="0061">an antigen from <i>Chlamydia trachomatis </i>[e.g. WO99/28475]. </li><li id="ul0002-0016" num="0062">an antigen from <i>Porphyromonas gingivalis </i>[e.g. Ross et al. (2001) <i>Vaccine </i>19:4135-4142].</li><li id="ul0002-0017" num="0063">polio antigen(s) [e.g. Sutter et al. (2000) <i>Pediatr Clin North Am </i>47:287-308; Zimmerman &amp; Spann (1999) <i>Am Fam Physician </i>59:113-118, 125-126] such as IPV or OPV.</li><li id="ul0002-0018" num="0064">rabies antigen(s) [e.g. Dreesen (1997) <i>Vaccine </i>15 Suppl:S2-6] such as lyophilised inactivated virus [e.g. MMWR Morb Mortal Wkly Rep 1998 Jan. 16; 47(1):12, 19; RabAvert™].</li><li id="ul0002-0019" num="0065">measles, mumps and/or rubella antigens [e.g. chapters 9, 10 &amp; 11 of Plotkin &amp; Mortimer].</li><li id="ul0002-0020" num="0066">influenza antigen(s) [e.g. chapter 19 of Plotkin &amp; Mortimer], such as the haemagglutinin and/or neuramimidase surface proteins.</li><li id="ul0002-0021" num="0067">an antigen from <i>Moraxella catarrhalis </i>[e.g. McMichael (2000) <i>Vaccine </i>19 Suppl 1:S101-107].</li><li id="ul0002-0022" num="0068">an antigen from <i>Staphylococcus aureus </i>[e.g. Kuroda et al. (2001) <i>Lancet </i>357(9264): 1225-1240; see also pages 1218-1219].</li></ul></li></ul>

Where a saccharide or carbohydrate antigen is included, it is preferably conjugated to a carrier protein in order to enhance immunogenicity [e.g. Ramsay et al. (2001) <i>Lancet </i>357(9251):195-196; Lindberg (1999) <i>Vaccine </i>17 Suppl 2:S28-36; Conjugate Vaccines (eds. Cruse et al.) ISBN 3805549326, particularly vol. 10:48-114 etc.]. Preferred carrier proteins are bacterial toxins or toxoids, such as diphtheria or tetanus toxoids. The CRM₁₉₇diphtheria toxoid is particularly preferred. Other suitable carrier proteins include the <i>N. meningitidis </i>outer membrane protein [e.g. EP-0372501], synthetic peptides [e.g. EP-0378881, EP-0427347], heat shock proteins [e.g. WO93/17712], pertussis proteins [e.g. WO98/58668; EP-0471177], protein D from <i>H. influenzae </i>[e.g. WO00/56360], toxin A or B from <i>C. difficile </i>[e.g. WO00/61761], etc. Any suitable conjugation reaction can be used, with any suitable linker where necessary.

Toxic protein antigens may be detoxified where necessary (e.g. detoxification of pertussis toxin by chemical and/or genetic means).

Where a diphtheria antigen is included in the composition it is preferred also to include tetanus antigen and pertussis antigens. Similarly, where a tetanus antigen is included it is preferred also to include diphtheria and pertussis antigens. Similarly, where a pertussis antigen is included it is preferred also to include diphtheria and tetanus antigens.

Antigens are preferably adsorbed to an aluminium salt.

Antigens in the composition will typically be present at a concentration of at least 1 μg/ml each. In general, the concentration of any given antigen will be sufficient to elicit an immune response against that antigen.

The invention also provides compositions comprising two or more proteins of the present invention.

The two or more proteins may comprise GBS sequences or may comprise GAS and GBS sequences.

A summary of standard techniques and procedures which may be employed to perform the invention (e.g. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows. This summary is not a limitation on the invention but, rather, gives examples that may be used, but are not required.

General

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature eg. Sambrook <i>Molecular Cloning, A Laboratory Manual, Second Edition </i>(1989); <i>DNA Cloning, Volumes I and II </i>(D. N Glover ed. 1985); <i>Oligonucleotide Synthesis </i>(M. J. Gait ed, 1984); <i>Nucleic Acid Hybridization </i>(B. D. Hames &amp; S. J. Higgins eds. 1984); <i>Transcription and Translation </i>(B. D. Hames &amp; S. J. Higgins eds. 1984); <i>Animal Cell Culture </i>(R. I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, <i>A Practical Guide to Molecular Cloning </i>(1984); the <i>Methods in Enzymology </i>series (Academic Press, Inc.), especially volumes 154 &amp; 155<i>; Gene Transfer Vectors for Mammalian Cells </i>(J. H. Miller and M. P. Calos eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker, eds. (1987), <i>Immunochemical Methods in Cell and Molecular Biology </i>(Academic Press, London); Scopes, (1987) <i>Protein Purification: Principles and Practice</i>, Second Edition (Springer-Verlag, N.Y.), and <i>Handbook of Experimental Immunology</i>, Volumes I-IV (D. M. Weir and C. C. Blackwell eds 1986).

Standard abbreviations for nucleotides and amino acids are used in this specification.

DEFINITIONS

A composition containing X is “substantially free of” Y when at least 85% by weight of the total X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95% or even 99% by weight.

The term “comprising” means “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.

The term “heterologous” refers to two biological components that are not found together in nature. The components may be host cells, genes, or regulatory regions, such as promoters. Although the heterologous components are not found together in nature, they can function together, as when a promoter heterologous to a gene is operably linked to the gene. Another example is where a <i>streptococcus </i>sequence is heterologous to a mouse host cell. A further examples would be two epitopes from the same or different proteins which have been assembled in a single protein in an arrangement not found in nature.

An “origin of replication” is a polynucleotide sequence that initiates and regulates replication of polynucleotides, such as an expression vector. The origin of replication behaves as an autonomous unit of polynucleotide replication within a cell, capable of replication under its own control. An origin of replication may be needed for a vector to replicate in a particular host cell. With certain origins of replication, an expression vector can be reproduced at a high copy number in the presence of the appropriate proteins within the cell. Examples of origins are the autonomously replicating sequences, which are effective in yeast; and the viral T-antigen, effective in COS-7 cells.

A “mutant” sequence is defined as DNA, RNA or amino acid sequence differing from but having sequence identity with the native or disclosed sequence. Depending on the particular sequence, the degree of sequence identity between the native or disclosed sequence and the mutant sequence is preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%, 99% or more, calculated using the Smith-Waterman algorithm as described above). As used herein, an “allelic variant” of a nucleic acid molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid molecule, or region, that occurs essentially at the same locus in the genome of another or second isolate, and that, due to natural variation caused by, for example, mutation or recombination, has a similar but not identical nucleic acid sequence. A coding region allelic variant typically encodes a protein having similar activity to that of the protein encoded by the gene to which it is being compared. An allelic variant can also comprise an alteration in the 5′ or 3′ untranslated regions of the gene, such as in regulatory control regions (eg. see U.S. Pat. No. 5,753,235).

Expression Systems

The <i>streptococcus </i>nucleotide sequences can be expressed in a variety of different expression systems; for example those used with mammalian cells, baculoviruses, plants, bacteria, and yeast.

i. Mammalian Systems

Mammalian expression systems are known in the art. A mammalian promoter is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5′ end of the coding sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element, usually located within 100 to 200 bp upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation [Sambrook et al. (1989) “Expression of Cloned Genes in Mammalian Cells.” In <i>Molecular Cloning: A Laboratory Manual, </i>2<i>nd ed]. </i>

Mammalian viral genes are often highly expressed and have a broad host range; therefore sequences encoding mammalian viral genes provide particularly useful promoter sequences. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter (Ad MLP), and herpes simplex virus promoter. In addition, sequences derived from non-viral genes, such as the murine metallotheionein gene, also provide useful promoter sequences. Expression may be either constitutive or regulated (inducible), depending on the promoter can be induced with glucocorticoid in hormone-responsive cells.

The presence of an enhancer element (enhancer), combined with the promoter elements described above, will usually increase expression levels. An enhancer is a regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to homologous or heterologous promoters, with synthesis beginning at the normal RNA start site. Enhancers are also active when they are placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation, or at a distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987) <i>Science </i>236:1237; Alberts et al. (1989) <i>Molecular Biology of the Cell, </i>2nd ed.]. Enhancer elements derived from viruses may be particularly useful, because they usually have a broader host range. Examples include the SV40 early gene enhancer [Dijkema et al (1985) <i>EMBO J. </i>4:761] and the enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus [Gorman et al. (1982b) <i>Proc. Natl. Acad. Sci. </i>79:6777] and from human cytomegalovirus [Boshart et al. (1985) <i>Cell </i>41:521]. Additionally, some enhancers are regulatable and become active only in the presence of an inducer, such as a hormone or metal ion [Sassone-Corsi and Borelli (1986) <i>Trends Genet. </i>2:215; Maniatis et al. (1987) <i>Science </i>236:1237].

A DNA molecule may be expressed intracellularly in mammalian cells. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in mammalian cells. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The adenovirus triparite leader is an example of a leader sequence that provides for secretion of a foreign protein in mammalian cells.

Usually, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3′ to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3′ terminus of the mature mRNA is formed by site-specific post-transcriptional cleavage and polyadenylation [Birnstiel et al. (1985) <i>Cell </i>41:349; Proudfoot and Whitelaw (1988) “Termination and 3′ end processing of eukaryotic RNA. In <i>Transcription and splicing </i>(ed. B. D. Hames and D. M. Glover); Proudfoot (1989) <i>Trends Biochem. Sci. </i>14:105]. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation signals include those derived from SV40 [Sambrook et al (1989) “Expression of cloned genes in cultured mammalian cells.” In <i>Molecular Cloning: A Laboratory Manual]. </i>

Usually, the above described components, comprising a promoter, polyadenylation signal, and transcription termination sequence are put together into expression constructs. Enhancers, introns with functional splice donor and acceptor sites, and leader sequences may also be included in an expression construct, if desired. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as mammalian cells or bacteria. Mammalian replication systems include those derived from animal viruses, which require trans-acting factors to replicate. For example, plasmids containing the replication systems of papovaviruses, such as SV40 [Gluzman (1981) <i>Cell </i>23:175] or polyomavirus, replicate to extremely high copy number in the presence of the appropriate viral T antigen. Additional examples of mammalian replicons include those derived from bovine papillomavirus and Epstein-Barr virus. Additionally, the replicon may have two replication systems, thus allowing it to be maintained, for example, in mammalian cells for expression and in a prokaryotic host for cloning and amplification. Examples of such mammalian-bacteria shuttle vectors include pMT2 [Kaufman et al. (1989) <i>Mol. Cell. Biol. </i>9:946] and pHEBO [Shimizu et al. (1986) <i>Mol. Cell. Biol. </i>6:1074].

The transformation procedure used depends upon the host to be transformed. Methods for introduction of heterologous polynucleotides into mammalian cells are known in the art and include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. Hep G2), and a number of other cell lines.

ii. Baculovirus Systems

The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector, and is operably linked to the control elements within that vector. Vector construction employs techniques which are known in the art. Generally, the components of the expression system include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus genome, and a convenient restriction site for insertion of the heterologous gene or genes to be expressed; a wild type baculovirus with a sequence homologous to the baculovirus-specific fragment in the transfer vector (this allows for the homologous recombination of the heterologous gene in to the baculovirus genome); and appropriate insect host cells and growth media.

After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the wild type viral genome are transfected into an insect host cell where the vector and viral genome are allowed to recombine. The packaged recombinant virus is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego Calif. (“MaxBac” kit). These techniques are generally known to those skilled in the art and fully described in Summers and Smith, <i>Texas Agricultural Experiment Station Bulletin No. </i>1555 (1987) (hereinafter “Summers and Smith”).

Prior to inserting the DNA sequence encoding the protein into the baculovirus genome, the above described components, comprising a promoter, leader (if desired), coding sequence, and transcription termination sequence, are usually assembled into an intermediate transplacement construct (transfer vector). This may contain a single gene and operably linked regulatory elements; multiple genes, each with its owned set of operably linked regulatory elements; or multiple genes, regulated by the same set of regulatory elements. Intermediate transplacement constructs are often maintained in a replicon, such as an extra-chromosomal element (e.g. plasmids) capable of stable maintenance in a host, such as a bacterium. The replicon will have a replication system, thus allowing it to be maintained in a suitable host for cloning and amplification.

Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373. Many other vectors, known to those of skill in the art, have also been designed. These include, for example, pVL985 (which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 basepairs downstream from the ATT; see Luckow and Summers, <i>Virology </i>(1989) 17:31.

The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) <i>Ann. Rev. Microbiol., </i>42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in <i>E. coli. </i>

Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream (5′ to 3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A baculovirus transfer vector may also have a second domain called an enhancer, which, if present, is usually distal to the structural gene. Expression may be either regulated or constitutive.

Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly useful promoter sequences. Examples include sequences derived from the gene encoding the viral polyhedron protein, Friesen et al., (1986) “The Regulation of Baculovirus Gene Expression,” in: <i>The Molecular Biology of Baculoviruses </i>(ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155 476; and the gene encoding the p10 protein, Vlak et al., (1988), <i>J. Gen. Virol. </i>69:765.

DNA encoding suitable signal sequences can be derived from genes for secreted insect or baculovirus proteins, such as the baculovirus polyhedrin gene (Carbonell et al. (1988) <i>Gene, </i>73:409). Alternatively, since the signals for mammalian cell posttranslational modifications (such as signal peptide cleavage, proteolytic cleavage, and phosphorylation) appear to be recognized by insect cells, and the signals required for secretion and nuclear accumulation also appear to be conserved between the invertebrate cells and vertebrate cells, leaders of non-insect origin, such as those derived from genes encoding human α-interferon, Maeda et al., (1985), <i>Nature </i>315:592; human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), <i>Molec. Cell. Biol. </i>8:3129; human IL-2, Smith et al., (1985) <i>Proc. Nat'l Acad. Sci. USA, </i>82:8404; mouse IL-3, (Miyajima et al., (1987) <i>Gene </i>58:273; and human glucocerebrosidase, Martin et al. (1988) <i>DNA, </i>7:99, can also be used to provide for secretion in insects.

A recombinant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed with the proper regulatory sequences, it can be secreted. Good intracellular expression of nonfused foreign proteins usually requires heterologous genes that ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. If desired, methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with cyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted from the insect cell by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in insects. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the translocation of the protein into the endoplasmic reticulum.

After insertion of the DNA sequence and/or the gene encoding the expression product precursor of the protein, an insect cell host is co-transformed with the heterologous DNA of the transfer vector and the genomic DNA of wild type baculovirus—usually by co-transfection. The promoter and transcription termination sequence of the construct will usually comprise a 2-5 kb section of the baculovirus genome. Methods for introducing heterologous DNA into the desired site in the baculovirus virus are known in the art. (See Summers and Smith supra; Ju et al. (1987); Smith et al., <i>Mol. Cell. Biol</i>. (1983) 3:2156; and Luckow and Summers (1989)). For example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover recombination; insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene. Miller et al., (1989), <i>Bioessays </i>4:91. The DNA sequence, when cloned in place of the polyhedrin gene in the expression vector, is flanked both 5′ and 3′ by polyhedrin-specific sequences and is positioned downstream of the polyhedrin promoter.

The newly formed baculovirus expression vector is subsequently packaged into an infectious recombinant baculovirus. Homologous recombination occurs at low frequency (between about 1% and about 5%); thus, the majority of the virus produced after cotransfection is still wild-type virus. Therefore, a method is necessary to identify recombinant viruses. An advantage of the expression system is a visual screen allowing recombinant viruses to be distinguished. The polyhedrin protein, which is produced by the native virus, is produced at very high levels in the nuclei of infected cells at late times after viral infection. Accumulated polyhedrin protein forms occlusion bodies that also contain embedded particles. These occlusion bodies, up to 15 μm in size, are highly refractile, giving them a bright shiny appearance that is readily visualized under the light microscope. Cells infected with recombinant viruses lack occlusion bodies. To distinguish recombinant virus from wild-type virus, the transfection supernatant is plaqued onto a monolayer of insect cells by techniques known to those skilled in the art. Namely, the plaques are screened under the light microscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant virus) of occlusion bodies. “Current Protocols in Microbiology” Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990); Summers and Smith, supra; Miller et al. (1989).

Recombinant baculovirus expression vectors have been developed for infection into several insect cells. For example, recombinant baculoviruses have been developed for, inter alia: <i>Aedes aegypti, Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda</i>, and <i>Trichoplusia ni </i>(WO 89/046699; Carbonell et al., (1985) <i>J. Virol. </i>56:153; Wright (1986) <i>Nature </i>321:718; Smith et al., (1983) <i>Mol. Cell. Biol. </i>3:2156; and see generally, Fraser, et al. (1989) <i>In Vitro Cell. Dev. Biol. </i>25:225).

Cells and cell culture media are commercially available for both direct and fusion expression of heterologous polypeptides in a baculovirus/expression system; cell culture technology is generally known to those skilled in the art. See, eg. Summers and Smith supra.

The modified insect cells may then be grown in an appropriate nutrient medium, which allows for stable maintenance of the plasmid(s) present in the modified insect host. Where the expression product gene is under inducible control, the host may be grown to high density, and expression induced. Alternatively, where expression is constitutive, the product will be continuously expressed into the medium and the nutrient medium must be continuously circulated, while removing the product of interest and augmenting depleted nutrients. The product may be purified by such techniques as chromatography, eg HPLC, affinity chromatography, ion exchange chromatography, etc.; electrophoresis; density gradient centrifugation; solvent extraction, etc. As appropriate, the product may be further purified, as required, so as to remove substantially any insect proteins which are also present in the medium, so as to provide a product which is at least substantially free of host debris, eg. proteins, lipids and polysaccharides.

In order to obtain protein expression, recombinant host cells derived from the transformants are incubated under conditions which allow expression of the recombinant protein encoding sequence. These conditions will vary, dependent upon the host cell selected. However, the conditions are readily ascertainable to those of ordinary skill in the art, based upon what is known in the art.

iii. Plant Systems

There are many plant cell culture and whole plant genetic expression systems known in the art. Exemplary plant cellular genetic expression systems include those described in patents, such as: U.S. Pat. Nos. 5,693,506; 5,659,122; and 5,608,143. Additional examples of genetic expression in plant cell culture has been described by Zenk, <i>Phytochemistry </i>30:3861-3863 (1991). Descriptions of plant protein signal peptides may be found in addition to the references described above in Vaulcombe et al., <i>Mol. Gen. Genet. </i>209:33-40 (1987); Chandler et al., <i>Plant Molecular Biology </i>3:407-418 (1984); Rogers, <i>J. Biol. Chem. </i>260:3731-3738 (1985); Rothstein et al., <i>Gene </i>55:353-356 (1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987); Wirsel et al., <i>Molecular Microbiology </i>3:3-14 (1989); Yu et al., <i>Gene </i>122:247-253 (1992). A description of the regulation of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by gibberellic acid can be found in R. L. Jones and J. MacMillin, Gibberellins: in: <i>Advanced Plant Physiology</i>, Malcolm B. Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52. References that describe other metabolically-regulated genes: Sheen, <i>Plant Cell, </i>2:1027-1038 (1990); Maas et al., <i>EMBO J. </i>9:3447-3452 (1990); Benkel and Hickey, <i>Proc. Natl. Acad. Sci. </i>84:1337-1339 (1987).

Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an expression cassette comprising genetic regulatory elements designed for operation in plants. The expression cassette is inserted into a desired expression vector with companion sequences upstream and downstream from the expression cassette suitable for expression in a plant host. The companion sequences will be of plasmid or viral origin and provide necessary characteristics to the vector to permit the vectors to move DNA from an original cloning host, such as bacteria, to the desired plant host. The basic bacterial/plant vector construct will preferably provide a broad host range prokaryote replication origin; a prokaryote selectable marker; and, for <i>Agrobacterium </i>transformations, T DNA sequences for <i>Agrobacterium</i>-mediated transfer to plant chromosomes. Where the heterologous gene is not readily amenable to detection, the construct will preferably also have a selectable marker gene suitable for determining if a plant cell has been transformed. A general review of suitable markers, for example for the members of the grass family, is found in Wilmink and Dons, 1993, <i>Plant Mol. Biol. Reptr, </i>11(2):165-185.

Sequences suitable for permitting integration of the heterologous sequence into the plant genome are also recommended. These might include transposon sequences and the like for homologous recombination as well as Ti sequences which permit random insertion of a heterologous expression cassette into a plant genome. Suitable prokaryote selectable markers include resistance toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions may also be present in the vector, as is known in the art.

The nucleic acid molecules of the subject invention may be included into an expression cassette for expression of the protein(s) of interest. Usually, there will be only one expression cassette, although two or more are feasible. The recombinant expression cassette will contain in addition to the heterologous protein encoding sequence the following elements, a promoter region, plant 5′ untranslated sequences, initiation codon depending upon whether or not the structural gene comes equipped with one, and a transcription and translation termination sequence. Unique restriction enzyme sites at the 5′ and 3′ ends of the cassette allow for easy insertion into a pre-existing vector.

A heterologous coding sequence may be for any protein relating to the present invention. The sequence encoding the protein of interest will encode a signal peptide which allows processing and translocation of the protein, as appropriate, and will usually lack any sequence which might result in the binding of the desired protein of the invention to a membrane. Since, for the most part, the transcriptional initiation region will be for a gene which is expressed and translocated during germination, by employing the signal peptide which provides for translocation, one may also provide for translocation of the protein of interest. In this way, the protein(s) of interest will be translocated from the cells in which they are expressed and may be efficiently harvested. Typically secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the seed. While it is not required that the protein be secreted from the cells in which the protein is produced, this facilitates the isolation and purification of the recombinant protein.

Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable to determine whether any portion of the cloned gene contains sequences which will be processed out as introns by the host's splicosome machinery. If so, site-directed mutagenesis of the “intron” region may be conducted to prevent losing a portion of the genetic message as a false intron code, Reed and Maniatis, <i>Cell </i>41:95-105, 1985.

The vector can be microinjected directly into plant cells by use of micropipettes to mechanically transfer the recombinant DNA. Crossway, <i>Mol. Gen. Genet, </i>202:179-185, 1985. The genetic material may also be transferred into the plant cell by using polyethylene glycol, Krens, et al., <i>Nature, </i>296, 72-74, 1982. Another method of introduction of nucleic acid segments is high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface, Klein, et al., <i>Nature, </i>327, 70-73, 1987 and Knudsen and Muller, 1991, <i>Planta, </i>185:330-336 teaching particle bombardment of barley endosperm to create transgenic barley. Yet another method of introduction would be fusion of protoplasts with other entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., <i>Proc. Natl. Acad. Sci. USA, </i>79, 1859-1863, 1982.

The vector may also be introduced into the plant cells by electroporation. (Fromm et al., <i>Proc. Natl. Acad. Sci. USA </i>82:5824, 1985). In this technique, plant protoplasts are electroporated in the presence of plasmids containing the gene construct. Electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electroporated plant protoplasts reform the cell wall, divide, and form plant callus.

All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be transformed by the present invention so that whole plants are recovered which contain the transferred gene. It is known that practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugarcane, sugar beet, cotton, fruit and other trees, legumes and vegetables. Some suitable plants include, for example, species from the genera <i>Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersion, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum</i>, and <i>Datura. </i>

Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts containing copies of the heterologous gene is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos germinate as natural embryos to form plants. The culture media will generally contain various amino acids and hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Shoots and roots normally develop simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. If these three variables are controlled, then regeneration is fully reproducible and repeatable.

In some plant cell culture systems, the desired protein of the invention may be excreted or alternatively, the protein may be extracted from the whole plant. Where the desired protein of the invention is secreted into the medium, it may be collected. Alternatively, the embryos and embryoless-half seeds or other plant tissue may be mechanically disrupted to release any secreted protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve soluble proteins. Conventional protein isolation and purification methods will be then used to purify the recombinant protein. Parameters of time, temperature pH, oxygen, and volumes will be adjusted through routine methods to optimize expression and recovery of heterologous protein.

iv. Bacterial Systems

Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence capable of binding bacterial RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation may be achieved by a gene activator protein binding sequence, which, if present is usually proximal (5′) to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in <i>Escherichia coli </i>(<i>E. coli</i>) [Raibaud et al. (1984) <i>Annu. Rev. Genet. </i>18:173]. Regulated expression may therefore be either positive or negative, thereby either enhancing or reducing transcription.

Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) [Chang et al. (1977) <i>Nature </i>198:1056], and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al. (1980) <i>Nuc. Acids Res. </i>8:4057; Yelverton et al. (1981) <i>Nucl. Acids Res. </i>9:731; U.S. Pat. No. 4,738,921; EP-A-0036776 and EP-A-0121775]. The g-laotamase (bla) promoter system [Weissmann (1981) “The cloning of interferon and other mistakes.” In <i>Interferon </i>3 (ed. I. Gresser)], bacteriophage lambda PL [Shimatake et al. (1981) <i>Nature </i>292:128] and T5 [U.S. Pat. No. 4,689,406] promoter systems also provide useful promoter sequences.

In addition, synthetic promoters which do not occur in nature also function as bacterial promoters. For example, transcription activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433]. For example, the tac promoter is a hybrid trp-lac promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac repressor [Amann et al. (1983) <i>Gene </i>25:167; de Boer et al. (1983) <i>Proc. Natl. Acad. Sci. </i>80:21]. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non-bacterial origin can also be coupled with a compatible RNA polymerase to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymerase/promoter system is an example of a coupled promoter system [Studier et al. (1986) <i>J. Mol. Biol. </i>189:113; Tabor et al. (1985) <i>Proc Natl. Acad. Sci. </i>82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an <i>E. coli </i>operator region (EPO-A-0 267 851).

In addition to a functioning promoter sequence, an efficient ribosome binding site is also useful for the expression of foreign genes in prokaryotes. In <i>E. coli</i>, the ribosome binding site is called the Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975) <i>Nature </i>254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the SD sequence and the 3′ and of <i>E. coli </i>16S rRNA [Steitz et al. (1979) “Genetic signals and nucleotide sequences in messenger RNA.” In <i>Biological Regulation and Development: Gene Expression </i>(ed. R. F. Goldberger)]. To express eukaryotic genes and prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) “Expression of cloned genes in <i>Escherichia coli</i>.” In <i>Molecular Cloning: A Laboratory Manual]. </i>

A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo on in vitro incubation with a bacterial methionine N-terminal peptidase (EP-A-0 219 237).

Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the N-terminal portion of an endogenous bacterial protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the bacteriophage lambda cell gene can be linked at the 5′ terminus of a foreign gene and expressed in bacteria. The resulting fusion protein preferably retains a site for a processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene [Nagai et al. (1984) <i>Nature </i>309:810]. Fusion proteins can also be made with sequences from the lacZ [Jia et al. (1987) <i>Gene </i>60:197], trpE [Allen et al. (1987) <i>J. Biotechnol. </i>5:93; Makoff et al. (1989) <i>J. Gen. Microbiol. </i>135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin specific processing-protease) to cleave the ubiquitin from the foreign protein. Through this method, native foreign protein can be isolated [Miller et al. (1989) <i>Bio/Technology </i>7:698].

Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules that encode a fusion protein comprised of a signal peptide sequence fragment that provides for secretion of the foreign protein in bacteria [U.S. Pat. No. 4,336,336]. The signal sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably there are processing sites, which can be cleaved either in vivo or in vitro encoded between the signal peptide fragment and the foreign gene.

DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins, such as the <i>E. coli </i>outer membrane protein gene (ompA) [Masui et al. (1983), in: <i>Experimental Manipulation of Gene Expression</i>; Ghrayeb et al. (1984) <i>EMBO J. </i>3:2437] and the <i>E. coli </i>alkaline phosphatase signal sequence (phoA) [Oka et al. (1985) <i>Proc. Natl. Acad. Sci. </i>82:7212]. As an additional example, the signal sequence of the alpha-amylase gene from various <i>Bacillus </i>strains can be used to secrete heterologous proteins from <i>B. subtilis </i>[Palva et al. (1982) <i>Proc. Natl. Acad. Sci. USA </i>79:5582; EP-A-0 244 042].

Usually, transcription termination sequences recognized by bacteria are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Transcription termination sequences frequently include DNA sequences of about 50 nucleotides capable of forming stem loop structures that aid in terminating transcription. Examples include transcription termination sequences derived from genes with strong promoters, such as the trp gene in <i>E. coli </i>as well as other biosynthetic genes.

Usually, the above described components, comprising a promoter, signal sequence (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will have a replication system, thus allowing it to be maintained in a prokaryotic host either for expression or for cloning and amplification. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably contain at least about 10, and more preferably at least about 20 plasmids. Either a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host.

Alternatively, the expression constructs can be integrated into the bacterial genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to the bacterial chromosome that allows the vector to integrate. Integrations appear to result from recombinations between homologous DNA in the vector and the bacterial chromosome. For example, integrating vectors constructed with DNA from various <i>Bacillus </i>strains integrate into the <i>Bacillus </i>chromosome (EP-A-0 127 328). Integrating vectors may also be comprised of bacteriophage or transposon sequences.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of bacterial strains that have been transformed. Selectable markers can be expressed in the bacterial host and may include genes which render bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline [Davies et al. (1978) <i>Annu. Rev. Microbiol. </i>32:469]. Selectable markers may also include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.

Alternatively, some of the above described components can be put together in transformation vectors. Transformation vectors are usually comprised of a selectable market that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extra-chromosomal replicons or integrating vectors, have been developed for transformation into many bacteria. For example, expression vectors have been developed for, inter alia, the following bacteria: <i>Bacillus subtilis </i>[Palva et al. (1982) <i>Proc. Natl. Acad. Sci. USA </i>79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541], <i>Escherichia coli </i>[Shimatake et al. (1981) <i>Nature </i>292:128; Amann et al. (1985) <i>Gene </i>40:183; Studier et al. (1986) <i>J. Mol. Biol. </i>189:113; EP-A-0 036 776, EP-A-0 136 829 and EP-A-0 136 907], <i>Streptococcus cremoris </i>[Powell et al. (1988) <i>Appl. Environ. Microbiol. </i>54:655]; <i>Streptococcus lividans </i>[Powell et al. (1988) <i>Appl. Environ. Microbiol. </i>54:655], <i>Streptomyces lividans </i>[U.S. Pat. No. 4,745,056].

Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually include either the transformation of bacteria treated with CaCl₂or other agents, such as divalent cations and DMSO. DNA can also be introduced into bacterial cells by electroporation. Transformation procedures usually vary with the bacterial species to be transformed. See eg. [Masson et al. (1989) <i>FEMS Microbiol. Lett. </i>60:273; Palva et al. (1982) <i>Proc. Natl. Acad. Sci. USA </i>79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541, <i>Bacillus</i>], [Miller et al. (1988) <i>Proc. Natl. Acad. Sci. </i>85:856; Wang et al. (1990) <i>J. Bacteriol. </i>172:949, <i>Campylobacter</i>], [Cohen et al. (1973) <i>Proc. Natl. Acad. Sci. </i>69:2110; Dower et al. (1988) <i>Nucleic Acids Res. </i>16:6127; Kushner (1978) “An improved method for transformation of <i>Escherichia coli </i>with ColE1-derived plasmids. In <i>Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering </i>(eds. H. W. Boyer and S. Nicosia); Mandel et al. (1970) <i>J. Mol. Biol. </i>53:159; Taketo (1988) <i>Biochim. Biophys. Acta </i>949:318; <i>Escherichia</i>], [Chassy et al. (1987) <i>FEMS Microbiol. Lett. </i>44:173 <i>Lactobacillus</i>]; [Fiedler et al. (1988) <i>Anal. Biochem </i>170:38, <i>Pseudomonas</i>]; [Augustin et al. (1990) <i>FEMS Microbiol. Lett. </i>66:203, <i>Staphylococcus</i>], [Barany et al. (1980) <i>J. Bacteriol. </i>144:698; Harlander (1987) “Transformation of <i>Streptococcus lactis </i>by electroporation, in: <i>Streptococcal Genetics </i>(ed. J. Ferretti and R. Curtiss III); Perry et al. (1981) <i>Infect. Immun. </i>32:1295; Powell et al. (1988) <i>Appl. Environ. Microbiol. </i>54:655; Somkuti et al. (1987) <i>Proc. </i>4<i>th Evr. Cong. Biotechnology </i>1:412<i>, Streptococcus]. </i>

v. Yeast Expression

Yeast expression systems are also known to one of ordinary skill in the art. A yeast promoter is any DNA sequence capable of binding yeast RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site (the “TATA Box”) and a transcription initiation site. A yeast promoter may also have a second domain called an upstream activator sequence (UAS), which, if present, is usually distal to the structural gene. The UAS permits regulated (inducible) expression. Constitutive expression occurs in the absence of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or reducing transcription.

Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding enzymes in the metabolic pathway provide particularly useful promoter sequences. Examples include alcohol dehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH), hexokinase, phosphofructokinase, 3-phosphoglycerate mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast PHO5 gene, encoding acid phosphatase, also provides useful promoter sequences [Myanohara et al. (1983) <i>Proc. Natl. Acad. Sci. USA </i>80: 1].

In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For example, UAS sequences of one yeast promoter may be joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation region (U.S. Pat. Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters which consist of the regulatory sequences of either the ADH2, GAL4, GAL10, OR PHO5 genes, combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore, a yeast promoter can include naturally occurring promoters of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription. Examples of such promoters include, inter alia, [Cohen et al. (1980) <i>Proc. Natl. Acad. Sci. USA </i>77:1078; Henikoff et al. (1981) <i>Nature </i>283:835; Hollenberg et al. (1981) <i>Curr. Topics Microbiol. Immunol. </i>96:119; Hollenberg et al. (1979) “The Expression of Bacterial Antibiotic Resistance Genes in the Yeast <i>Saccharomyces cerevisiae</i>,” in: <i>Plasmids of Medical, Environmental and Commercial Importance </i>(eds. K. N. Timmis and A. Puhler); Mercerau-Puigalon et al. (1980) <i>Gene </i>11:163; Panthier et al. (1980) <i>Curr. Genet. </i>2:109;].

A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Fusion proteins provide an alternative for yeast expression systems, as well as in mammalian, baculovirus, and bacterial expression systems. Usually, a DNA sequence encoding the N-terminal portion of an endogenous yeast protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be linked at the 5′ terminus of a foreign gene and expressed in yeast. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin-specific processing protease) to cleave the ubiquitin from the foreign protein. Through this method, therefore, native foreign protein can be isolated (eg. WO88/024066).

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provide for secretion in yeast of the foreign protein. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell.

DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins, such as the yeast invertase gene (EP-A-0 012 873; JPO. 62,096,086) and the A-factor gene (U.S. Pat. No. 4,588,684). Alternatively, leaders of non-yeast origin, such as an interferon leader, exist that also provide for secretion in yeast (EP-A-0 060 057).

A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor gene, which contains both a “pre” signal sequence, and a “pro” region. The types of alpha-factor fragments that can be employed include the full-length pre-pro alpha factor leader (about 83 amino acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino acid residues) (U.S. Pat. Nos. 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing an alpha-factor leader fragment that provides for secretion include hybrid alpha-factor leaders made with a presequence of a first yeast, but a pro-region from a second yeast alphafactor. (eg. see WO 89/02463.)

Usually, transcription termination sequences recognized by yeast are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminator sequence and other yeast-recognized termination sequences, such as those coding for glycolytic enzymes.

Usually, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria. The replicon may have two replication systems, thus allowing it to be maintained, for example, in yeast for expression and in a prokaryotic host for cloning and amplification. Examples of such yeast-bacteria shuttle vectors include YEp24 [Botstein et al. (1979) <i>Gene </i>8:17-24], pCl/1 [Brake et al. (1984) <i>Proc. Natl. Acad. Sci USA </i>81:4642-4646], and YRp17 [Stinchcomb et al. (1982) <i>J. Mol. Biol. </i>158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably have at least about 10, and more preferably at least about 20. Enter a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host. See eg. Brake et al., supra.

Alternatively, the expression constructs can be integrated into the yeast genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to a yeast chromosome that allows the vector to integrate, and preferably contain two homologous sequences flanking the expression construct. Integrations appear to result from recombinations between homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al. (1983) <i>Methods in Enzymol. </i>101:228-245]. An integrating vector may be directed to a specific locus in yeast by selecting the appropriate homologous sequence for inclusion in the vector. See Orr-Weaver et al., supra. One or more expression construct may integrate, possibly affecting levels of recombinant protein produced [Rine et al. (1983) <i>Proc. Natl. Acad. Sci. USA </i>80:6750]. The chromosomal sequences included in the vector can occur either as a single segment in the vector, which results in the integration of the entire vector, or two segments homologous to adjacent segments in the chromosome and flanking the expression construct in the vector, which can result in the stable integration of only the expression construct.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of yeast strains that have been transformed. Selectable markers may include biosynthetic genes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2, TRP1, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide yeast with the ability to grow in the presence of toxic compounds, such as metal. For example, the presence of CUP1 allows yeast to grow in the presence of copper ions [Butt et al. (1987) <i>Microbiol, Rev. </i>51:351].

Alternatively, some of the above described components can be put together into transformation vectors. Transformation vectors are usually comprised of a selectable marker that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal replicons or integrating vectors, have been developed for transformation into many yeasts. For example, expression vectors have been developed for, inter alia, the following yeasts: <i>Candida albicans </i>[Kurtz, et al. (1986) <i>Mol. Cell. Biol. </i>6:142], <i>Candida maltosa </i>[Kunze, et al. (1985) <i>J. Basic Microbiol. </i>25:141]. <i>Hansenula polymorpha </i>[Gleeson, et al. (1986) <i>J. Gen. Microbiol. </i>132:3459; Roggenkamp et al. (1986) <i>Mol. Gen. Genet. </i>202:302], <i>Kluyveromyces fragilis </i>[Das, et al. (1984) <i>J. Bacteriol. </i>158:1165], <i>Kluyveromyces lactis </i>[De Louvencourt et al. (1983) <i>J. Bacteriol. </i>154:737; Van den Berg et al. (1990) <i>Bio/Technology </i>8:135], <i>Pichia guillerimondii </i>[Kunze et al. (1985) <i>J. Basic Microbiol. </i>25:141], <i>Pichia pastoris </i>[Cregg, et al. (1985) <i>Mol. Cell. Biol. </i>5:3376; U.S. Pat. Nos. 4,837,148 and 4,929,555], <i>Saccharomyces cerevisiae </i>[Hinnen et al. (1978) <i>Proc. Natl. Acad. Sci. USA </i>75:1929; Ito et al. (1983) <i>J. Bacteriol. </i>153:163], <i>Schizosaccharomyces pombe </i>[Beach and Nurse (1981) <i>Nature </i>300:706], and <i>Yarrowia lipolytica </i>[Davidow, et al. (1985) <i>Curr. Genet. </i>10:380471 Gaillardin, et al. (1985) <i>Curr. Genet. </i>10:49].

Methods of introducing exogenous DNA into yeast hosts are well-known in the art, and usually include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to be transformed. See eg. [Kurtz et al. (1986) <i>Mol. Cell. Biol. </i>6:142; Kunze et al. (1985) <i>J. Basic Microbiol. </i>25:141; <i>Candida</i>]; [Gleeson et al. (1986) <i>J. Gen. Microbiol. </i>132:3459; Roggenkamp et al. (1986) <i>Mol. Gen. Genet. </i>202:302; <i>Hansenula</i>]; [Das et al. (1984) <i>J. Bacteriol. </i>158:1165; De Louvencourt et al. (1983) <i>J. Bacteriol. </i>154:1165; Van den Berg et al. (1990) <i>Bio/Technology </i>8:135; <i>Kluyveromyces</i>]; [Cregg et al. (1985) <i>Mol. Cell. Biol. </i>5:3376; Kunze et al. (1985) <i>J. Basic Microbiol. </i>25:141; U.S. Pat. Nos. 4,837,148 and 4,929,555; <i>Pichia</i>]; [Hinnen et al. (1978) <i>Proc. Natl. Acad. Sci. USA </i>75; 1929; Ito et al. (1983) <i>J. Bacteriol. </i>153:163 <i>Saccharomyces</i>]; [Beach and Nurse (1981) <i>Nature </i>300:706; <i>Schizosaccharomyces</i>]; [Davidow et al. (1985) <i>Curr. Genet. </i>10:39; Gaillardin et al. (1985) <i>Curr. Genet. </i>10:49; <i>Yarrowia]. </i>

Antibodies

As used herein, the term “antibody” refers to a polypeptide or group of polypeptides composed of at least one antibody combining site. An “antibody combining site” is the three-dimensional binding space with an internal surface shape and charge distribution complementary to the features of an epitope of an antigen, which allows a binding of the antibody with the antigen. “Antibody” includes, for example, vertebrate antibodies, hybrid antibodies, chimeric antibodies, humanised antibodies, altered antibodies, univalent antibodies, Fab proteins, and single domain antibodies.

Antibodies against the proteins of the invention are useful for affinity chromatography, immunoassays, and distinguishing/identifying <i>streptococcus </i>proteins.

Antibodies to the proteins of the invention, both polyclonal and monoclonal, may be prepared by conventional methods. In general, the protein is first used to immunize a suitable animal, preferably a mouse, rat, rabbit or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat antibodies. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 μg/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization. Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25° C. for one hour, followed by incubating at 4° C. for 2-18 hours. The serum is recovered by centrifugation (eg. 1,000 g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the standard method of Kohler &amp; Milstein [<i>Nature </i>(1975) 256:495-96], or a modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well coated with the protein antigen. B-cells expressing membrane-bound immunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas, and are cultured in a selective medium (eg. hypoxanthine, aminopterin, thymidine medium, “HAT”). The resulting hybridomas are plated by limiting dilution, and are assayed for production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are then cultured either in vitro (eg. in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice).

If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly ³²P and ¹²⁵I), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3′,5,5′-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a spectrophotometer. “Specific binding partner” refers to a protein capable of binding a ligand molecule with high specificity, as for example in the case of an antigen and a monoclonal antibody specific therefor. Other specific binding partners include biotin and avidin or streptavidin, IgG and protein A, and the numerous receptor-ligand couples known in the art. It should be understood that the above description is not meant to categorize the various labels into distinct classes, as the same label may serve in several different modes. For example, ¹²⁵I may serve as a radioactive label or as an electron-dense reagent. HRP may serve as enzyme or as antigen for a MAb. Further, one may combine various labels for desired effect. For example, MAbs and avidin also require labels in the practice of this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled with ¹²⁵I, or with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be readily apparent to those of ordinary skill in the art, and are considered as equivalents within the scope of the instant invention.

Pharmaceutical Compositions

Pharmaceutical compositions can comprise either polypeptides, antibodies, or nucleic acid of the invention. The pharmaceutical compositions will comprise a therapeutically effective amount of either polypeptides, antibodies, or polynucleotides of the claimed invention.

The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased body temperature. The precise effective amount for a subject will depend upon the subject's size and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount in advance. However, the effective amount for a given situation can be determined by routine experimentation and is within the judgement of the clinician.

For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the molecule of the invention in the individual to which it is administered.

A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent, such as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus particles. Such carriers are well known to those of ordinary skill in the art.

Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).

Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles. Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier.

Delivery Methods

Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals; in particular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Vaccines

Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection).

Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with “pharmaceutically acceptable carriers,” which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Additionally, these carriers may function as immunostimulating agents (“adjuvants”). Furthermore, the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, <i>H. pylori</i>, etc. pathogens.

Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59™ (WO90/14837; Chapter 10 in <i>Vaccine Design—the subunit and adjuvant approach </i>(1995) ed. Powell &amp; Newman), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionally containing MTP-PE) formulated into submicron particles using a microfluidizer, (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-blocked polymer L121, and thr-MDP either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) Ribi™ adjuvant system (RAS), (Ribi Immunochem, Hamilton, Mont.) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (Detox™); (2) saponin adjuvants, such as QS21 or Stimulon™ (Cambridge Bioscience, Worcester, Mass.) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes), which ISCOMS may be devoid of additional detergent e.g. WO00/07621; (3) Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (4) cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 (WO99/44636), etc.), interferons (e.g. gamma interferon), macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc.; (5) monophosphoryl lipid A (MPL) or 3-O-deacylated MPL (3dMPL) e.g. GB-2220221, EP-A-0689454; (6) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions e.g. EP-A-0835318, EP-A-0735898, EP-A-0761231; (7) oligonucleotides comprising CpG motifs [Krieg Vaccine 2000, 19, 618-622; Krieg <i>Curr opin Mol Ther </i>2001 3:15-24; Roman et al., <i>Nat. Med., </i>1997, 3, 849-854; Weiner et al., <i>PNAS USA, </i>1997, 94, 10833-10837; Davis et al., <i>J. Immunol., </i>1998, 160, 870-876; Chu et al., <i>J. Exp. Med., </i>1997, 186, 1623-1631; Lipford et al., <i>Eur. J. Immunol., </i>1997, 27, 2340-2344; Moldoveanu et al., <i>Vaccine, </i>1988, 16, 1216-1224, Krieg et al., <i>Nature, </i>1995, 374, 546-549; Klinman et al., <i>PNAS USA, </i>1996, 93, 2879-2883; Ballas et al., <i>J. Immunol., </i>1996, 157, 1840-1845; Cowdery et al., <i>J. Immunol., </i>1996, 156, 4570-4575; Halpern et al., <i>Cell. Immunol., </i>1996, 167, 72-78; Yamamoto et al., <i>Jpn. J. Cancer Res., </i>1988, 79, 866-873; Stacey et al., <i>J. Immunol., </i>1996, 157, 2116-2122; Messina et al., <i>J. Immunol., </i>1991, 147, 1759-1764; Yi et al., <i>J. Immunol., </i>1996, 157, 4918-4925; Yi et al., <i>J. Immunol., </i>1996, 157, 5394-5402; Yi et al., <i>J. Immunol., </i>1998, 160, 4755-4761; and Yi et al., <i>J. Immunol., </i>1998, 160, 5898-5906; International patent applications WO96/02555, WO98/16247, WO98/18810, WO98/40100, WO98/55495, WO98/37919 and WO98/52581] i.e. containing at least one CG dinucleotide, with 5-methylcytosine optionally being used in place of cytosine; (8) a polyoxyethylene ether or a polyoxyethylene ester e.g. WO99/52549; (9) a polyoxyethylene sorbitan ester surfactant in combination with an octoxynol (e.g. WO01/21207) or a polyoxyethylene alkyl ether or ester surfactant in combination with at least one additional non-ionic surfactant such as an octoxynol (e.g. WO01/21152); (10) an immunostimulatory oligonucleotide (e.g. a CpG oligonucleotide) and a saponin e.g. WO00/62800; (11) an immunostimulant and a particle of metal salt e.g. WO00/23105; (12) a saponin and an oil-in-water emulsion e.g. WO99/11241; (13) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) e.g. WO98/57659; (14) aluminium salts, preferably hydroxide or phosphate, but any other suitable salt may also be used (e.g. hydroxyphosphate, oxyhydroxide, orthophosphate, sulphate etc. [e.g. see chapters 8 &amp; 9 of Powell &amp; Newman]). Mixtures of different aluminium salts may also be used. The salt may take any suitable form (e.g. gel, crystalline, amorphous etc.); (15) other substances that act as immunostimulating agents to enhance the efficacy of the composition. Aluminium salts and/or MF59™ are preferred.

As mentioned above, muramyl peptides include, but are not limited to, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.

The immunogenic compositions (eg. the immunising antigen/immunogen/polypeptide/protein/nucleic acid, pharmaceutically acceptable carrier, and adjuvant) typically will contain diluents, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.

Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for enhanced adjuvant effect, as discussed above under pharmaceutically acceptable carriers.

Immunogenic compositions used as vaccines comprise an immunologically effective amount of the antigenic or immunogenic polypeptides, as well as any other of the above-mentioned components, as needed. By “immunologically effective amount”, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated (eg. nonhuman primate, primate, etc.), the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other rel-evant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.

The immunogenic compositions are conventionally administered parenterally, eg. by injection, either subcutaneously, intramuscularly, or transdermally/transcutaneously (eg. WO98/20734). Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose schedule or a multiple dose schedule. The vaccine may be administered in conjunction with other immunoregulatory agents.

As an alternative to protein-based vaccines, DNA vaccination may be used [eg. Robinson &amp; Torres (1997) <i>Seminars in Immunol </i>9:271-283; Donnelly et al. (1997) <i>Annu Rev Immunol </i>15:617-648; later herein].

Gene Delivery Vehicles

Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of the invention, to be delivered to the mammal for expression in the mammal, can be administered either locally or systemically. These constructs can utilize viral or non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequence can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated.

The invention includes gene delivery vehicles capable of expressing the contemplated nucleic acid sequences. The gene delivery vehicle is preferably a viral vector and, more preferably, a retroviral, adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirus vector. The viral vector can also be an astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus, poxvirus, or togavirus viral vector. See generally, Jolly (1994) <i>Cancer Gene Therapy </i>1:51-64; Kimura (1994) <i>Human Gene Therapy </i>5:845-852; Connelly (1995) <i>Human Gene Therapy </i>6:185-193; and Kaplitt (1994) <i>Nature Genetics </i>6:148-153.

Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector is employable in the invention, including B, C and D type retroviruses, xenotropic retroviruses (for example, NZB-X1, NZB-X2 and NZB9-1 (see O'Neill (1985) <i>J. Virol. </i>53:160) polytropic retroviruses eg. MCF and MCF-MLV (see Kelly (1983) <i>J. Virol. </i>45:291), spumaviruses and lentiviruses. See RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.

Portions of the retroviral gene therapy vector may be derived from different retroviruses. For example, retrovector LTRs may be derived from a Murine Sarcoma Virus, a tRNA binding site from a Rous Sarcoma Virus, a packaging signal from a Murine Leukemia Virus, and an origin of second strand synthesis from an Avian Leukosis Virus.

These recombinant retroviral vectors may be used to generate transduction competent retroviral vector particles by introducing them into appropriate packaging cell lines (see U.S. Pat. No. 5,591,624). Retrovirus vectors can be constructed for site-specific integration into host cell DNA by incorporation of a chimeric integrase enzyme into the retroviral particle (see WO96/37626). It is preferable that the recombinant viral vector is a replication defective recombinant virus.

Packaging cell lines suitable for use with the above-described retrovirus vectors are well known in the art, are readily prepared (see WO95/30763 and WO92/05266), and can be used to create producer cell lines (also termed vector cell lines or “VCLs”) for the production of recombinant vector particles. Preferably, the packaging cell lines are made from human parent cells (eg. HT1080 cells) or mink parent cell lines, which eliminates inactivation in human serum.

Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian Leukosis Virus, Bovine Leukemia, Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Virus, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularly preferred Murine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe (1976) <i>J Virol </i>19:19-25), Abelson (ATCC No. VR-999), Friend (ATCC No. VR-245), Graffi, Gross (ATCC Nol VR-590), Kirsten, Harvey Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine Leukemia Virus (ATCC No. VR-190). Such retroviruses may be obtained from depositories or collections such as the American Type Culture Collection (“ATCC”) in Rockville, Md. or isolated from known sources using commonly available techniques.

Exemplary known retroviral gene therapy vectors employable in this invention include those described in patent applications GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468; WO89/05349, WO89/09271, WO90/02806, WO90/07936, WO94/03622, WO93/25698, WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825, WO95/07994, U.S. Pat. No. 5,219,740, U.S. Pat. Nos. 4,405,712, 4,861,719, 4,980,289, 4,777,127, 5,591,624. See also Vile (1993) <i>Cancer Res </i>53:3860-3864; Vile (1993) <i>Cancer Res </i>53:962-967; Ram (1993) <i>Cancer Res </i>53 (1993) 83-88; Takamiya (1992) <i>J Neurosci Res </i>33:493-503; Baba (1993) <i>J Neurosurg </i>79:729-735; Mann (1983) <i>Cell </i>33:153; Cane (1984) <i>Proc Natl Acad Sci </i>81:6349; and Miller (1990) <i>Human Gene Therapy </i>1.

Human adenoviral gene therapy vectors are also known in the art and employable in this invention. See, for example, Berkner (1988) <i>Biotechniques </i>6:616 and Rosenfeld (1991) <i>Science </i>252:431, and WO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral gene therapy vectors employable in this invention include those described in the above referenced documents and in WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655, WO95/27071, WO95/29993, WO95/34671, WO96/05320, WO94/08026, WO94/11506, WO93/06223, WO94/24299, WO95/14102, WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and WO95/09654. Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992) <i>Hum. Gene Ther. </i>3:147-154 may be employed. The gene delivery vehicles of the invention also include adenovirus associated virus (AAV) vectors. Leading and preferred examples of such vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava, WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in which the native D-sequences are modified by substitution of nucleotides, such that at least 5 native nucleotides and up to 18 native nucleotides, preferably at least 10 native nucleotides up to 18 native nucleotides, most preferably 10 native nucleotides are retained and the remaining nucleotides of the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the AAV inverted terminal repeats are sequences of 20 consecutive nucleotides in each AAV inverted terminal repeat (ie. there is one sequence at each end) which are not involved in HP formation. The non-native replacement nucleotide may be any nucleotide other than the nucleotide found in the native D-sequence in the same position. Other employable exemplary AAV vectors are pWP-19, pWN-1, both of which are disclosed in Nahreini (1993) <i>Gene </i>124:257-262. Another example of such an AAV vector is psub201 (see Samulski (1987) <i>J. Virol. </i>61:3096). Another exemplary AAV vector is the Double-D ITR vector. Construction of the Double-D ITR vector is disclosed in U.S. Pat. No. 5,478,745. Still other vectors are those disclosed in Carter U.S. Pat. No. 4,797,368 and Muzyczka U.S. Pat. No. 5,139,941, Chartejee U.S. Pat. No. 5,474,935, and Kotin WO94/288157. Yet a further example of an AAV vector employable in this invention is SSV9AFABTKneo, which contains the AFP enhancer and albumin promoter and directs expression predominantly in the liver. Its structure and construction are disclosed in Su (1996) <i>Human Gene Therapy </i>7:463-470. Additional AAV gene therapy vectors are described in U.S. Pat. Nos. 5,354,678, 5,173,414, 5,139,941, and 5,252,479.

The gene therapy vectors of the invention also include herpes vectors. Leading and preferred examples are herpes simplex virus vectors containing a sequence encoding a thymidine kinase polypeptide such as those disclosed in U.S. Pat. No. 5,288,641 and EP0176170 (Roizman). Additional exemplary herpes simplex virus vectors include HFEM/ICP6-LacZ disclosed in WO95/04139 (Wistar Institute), pHSVIac described in Geller (1988) <i>Science </i>241:1667-1669 and in WO90/09441 and WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) <i>Human Gene Therapy </i>3:11-19 and HSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), and those deposited with the ATCC with accession numbers VR-977 and VR-260.

Also contemplated are alpha virus gene therapy vectors that can be employed in this invention. Preferred alpha virus vectors are Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCC VR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373; ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCC VR-1250; ATCC VR-1249; ATCC VR-532), and those described in U.S. Pat. Nos. 5,091,309, 5,217,879, and WO92/10578. More particularly, those alpha virus vectors described in U.S. Ser. No. 08/405,627, filed Mar. 15, 1995, WO94/21792, WO92/10578, WO95/07994, U.S. Pat. Nos. 5,091,309 and 5,217,879 are employable. Such alpha viruses may be obtained from depositories or collections such as the ATCC in Rockville, Md. or isolated from known sources using commonly available techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see U.S. Ser. No. 08/679,640).

DNA vector systems such as eukaryotic layered expression systems are also useful for expressing the nucleic acids of the invention. See WO95/07994 for a detailed description of eukaryotic layered expression systems. Preferably, the eukaryotic layered expression systems of the invention are derived from alphavirus vectors and most preferably from Sindbis viral vectors.

Other viral vectors suitable for use in the present invention include those derived from poliovirus, for example ATCC VR-58 and those described in Evans, Nature 339 (1989) 385 and Sabin (1973) <i>J. Biol. Standardization </i>1:115; rhinovirus, for example ATCC VR-1110 and those described in Arnold (1990) <i>J Cell Biochem L</i>401; pox viruses such as canary pox virus or vaccinia virus, for example ATCC VR-111 and ATCC VR-2010 and those described in Fisher-Hoch (1989) <i>Proc Natl Acad Sci </i>86:317; Flexner (1989) <i>Ann NY Acad Sci </i>569:86, Flexner (1990) <i>Vaccine </i>8:17; in U.S. Pat. No. 4,603,112 and U.S. Pat. No. 4,769,330 and WO89/01973; SV40 virus, for example ATCC VR-305 and those described in Mulligan (1979) <i>Nature </i>277:108 and Madzak (1992) <i>J Gen Virol </i>73:1533; influenza virus, for example ATCC VR-797 and recombinant influenza viruses made employing reverse genetics techniques as described in U.S. Pat. No. 5,166,057 and in Enami (1990) <i>Proc Natl Acad Sci </i>87:3802-3805; Enami &amp; Palese (1991) <i>J Virol </i>65:2711-2713 and Luytjes (1989) <i>Cell </i>59:110, (see also McMichael (1983) <i>NEJ Med </i>309:13, and Yap (1978) <i>Nature </i>273:238 and Nature (1979) 277:108); human immunodeficiency virus as described in EP-0386882 and in Buchschacher (1992) <i>J. Virol. </i>66:2731; measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-0440219; Aura virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240; Cabassou virus, for example ATCC VR-922; Chikungunya virus, for example ATCC VR-64 and ATCC VR-1241; Fort Morgan Virus, for example ATCC VR-924; Getah virus, for example ATCC VR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927; Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCC VR-580 and ATCC VR-1244; Ndumu virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, for example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for example ATCC VR-374; Whataroa virus, for example ATCC VR-926; Y-62-33 virus, for example ATCC VR-375; O'Nyong virus, Eastern encephalitis virus, for example ATCC VR-65 and ATCC VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622 and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre (1966) <i>Proc Soc Exp Biol Med </i>121:190.

Delivery of the compositions of this invention into cells is not limited to the above mentioned viral vectors. Other delivery methods and media may be employed such as, for example, nucleic acid expression vectors, polycationic condensed DNA linked or unlinked to killed adenovirus alone, for example see U.S. Ser. No. 08/366,787, filed Dec. 30, 1994 and Curiel (1992) <i>Hum Gene Ther </i>3:147-154 ligand linked DNA, for example see Wu (1989) <i>J Biol Chem </i>264:16985-16987, eucaryotic cell delivery vehicles cells, for example see U.S. Ser. No. 08/240,030, filed May 9, 1994, and U.S. Ser. No. 08/404,796, deposition of photopolymerized hydrogel materials, hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655, ionizing radiation as described in U.S. Pat. No. 5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell membranes. Additional approaches are described in Philip (1994) <i>Mol Cell Biol </i>14:2411-2418 and in Woffendin (1994) <i>Proc Natl Acad Sci </i>91:1581-1585.

Particle mediated gene transfer may be employed, for example see U.S. Ser. No. 60/023,867. Briefly, the sequence can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, as described in Wu &amp; Wu (1987) <i>J. Biol. Chem. </i>262:4429-4432, insulin as described in Hucked (1990) <i>Biochem Pharmacol </i>40:253-263, galactose as described in Plank (1992) <i>Bioconjugate Chem </i>3:533-539, lactose or transferrin.

Naked DNA may also be employed. Exemplary naked DNA introduction methods are described in WO 90/11092 and U.S. Pat. No. 5,580,859. Uptake efficiency may be improved using biodegradable latex beads. DNA coated latex beads are efficiently transported into cells after endocytosis initiation by the beads. The method may be improved further by treatment of the beads to increase hydrophobicity and thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.

Liposomes that can act as gene delivery vehicles are described in U.S. Pat. No. 5,422,120, WO95/13796, WO94/23697, WO91/14445 and EP-524,968. As described in U.S. Ser. No. 60/023,867, on non-viral delivery, the nucleic acid sequences encoding a polypeptide can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then be incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, insulin, galactose, lactose, or transferrin. Other delivery systems include the use of liposomes to encapsulate DNA comprising the gene under the control of a variety of tissue-specific or ubiquitously-active promoters. Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in Woffendin et al (1994) <i>Proc. Natl. Acad. Sci. USA </i>91(24):11581-11585. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655; use of ionizing radiation for activating transferred gene, as described in U.S. Pat. No. 5,206,152 and WO92/11033

Exemplary liposome and polycationic gene delivery vehicles are those described in U.S. Pat. Nos. 5,422,120 and 4,762,915; in WO 95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry, pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) <i>Biochem Biophys Acta </i>600:1; Bayer (1979) <i>Biochem Biophys Acta </i>550:464; Rivnay (1987) <i>Meth Enzymol </i>149:119; Wang (1987) <i>Proc Natl Acad Sci </i>84:7851; Plant (1989) <i>Anal Biochem </i>176:420.

A polynucleotide composition can comprises therapeutically effective amount of a gene therapy vehicle, as the term is defined above. For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

Delivery Methods

Once formulated, the polynucleotide compositions of the invention can be administered (1) directly to the subject; (2) delivered ex vivo, to cells derived from the subject; or (3) in vitro for expression of recombinant proteins. The subjects to be treated can be mammals or birds. Also, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known in the art and described in eg. WO93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hematopoetic, lymph cells, macrophages, dendritic cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished by the following procedures, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well known in the art.

Polynucleotide and Polypeptide Pharmaceutical Compositions

In addition to the pharmaceutically acceptable carriers and salts described above, the following additional agents can be used with polynucleotide and/or polypeptide compositions.

A. Polypeptides

One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR); transferrin; asialoglycoproteins; antibodies; antibody fragments; ferritin; interleukins; interferons, granulocyte, macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and erythropoietin. Viral antigens, such as envelope proteins, can also be used. Also, proteins from other invasive organisms, such as the 17 amino acid peptide from the circumsporozoite protein of <i>plasmodium falciparum </i>known as RII.

B. Hormones, Vitamins, etc.

Other groups that can be included are, for example: hormones, steroids, androgens, estrogens, thyroid hormone, or vitamins, folic acid.

C. Polyalkylenes, Polysaccharides. Etc.

Also, polyalkylene glycol can be included with the desired polynucleotides/polypeptides. In a preferred embodiment, the polyalkylene glycol is polyethlylene glycol. In addition, mono-, di-, or polysaccharides can be included. In a preferred embodiment of this aspect, the polysaccharide is dextran or DEAE-dextran. Also, chitosan and poly(lactide-co-glycolide)

D. Lipids, and Liposomes

The desired polynucleotide/polypeptide can also be encapsulated in lipids or packaged in liposomes prior to delivery to the subject or to cells derived therefrom.

Lipid encapsulation is generally accomplished using liposomes which are able to stably bind or entrap and retain nucleic acid. The ratio of condensed polynucleotide to lipid preparation can vary but will generally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. For a review of the use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) <i>Biochim. Biophys. Acta. </i>1097:1-17; Straubinger (1983) <i>Meth. Enzymol. </i>101:512-527.

Liposomal preparations for use in the present invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Felgner (1987) <i>Proc. Natl. Acad. Sci. USA </i>84:7413-7416); mRNA (Malone (1989) <i>Proc. Natl. Acad. Sci. USA </i>86:6077-6081); and purified transcription factors (Debs (1990) <i>J. Biol. Chem. </i>265:10189-10192), in functional form.

Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethyl-ammonium (DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Felgner supra). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, eg. Szoka (1978) <i>Proc. Natl. Acad. Sci. USA </i>75:4194-4198; WO90/11092 for a description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.

Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.

The liposomes can comprise multilammelar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs). The various liposome-nucleic acid complexes are prepared using methods known in the art. See eg. Straubinger (1983) <i>Meth. Immunol. </i>101:512-527; Szoka (1978) <i>Proc. Natl. Acad. Sci. USA </i>75:4194-4198; Papahadjopoulos (1975) <i>Biochim. Biophys. Acta </i>394:483; Wilson (1979) <i>Cell </i>17:77); Deamer &amp; Bangham (1976) <i>Biochim. Biophys. Acta </i>443:629; Ostro (1977) <i>Biochem. Biophys. Res. Commun. </i>76:836; Fraley (1979) <i>Proc. Natl. Acad. Sci. USA </i>76:3348); Enoch &amp; Strittmatter (1979) <i>Proc. Natl. Acad. Sci. USA </i>76:145; Fraley (1980) <i>J. Biol. Chem</i>. (1980) 255:10431; Szoka &amp; Papahadjopoulos (1978) <i>Proc. Natl. Acad. Sci. USA </i>75:145; and Schaefer-Ridder (1982) <i>Science </i>215:166.

E. Lipoproteins

In addition, lipoproteins can be included with the polynucleotide/polypeptide to be delivered. Examples of lipoproteins to be utilized include: chylomicrons, HDL, IDL, LDL, and VLDL. Mutants, fragments, or fusions of these proteins can also be used. Also, modifications of naturally occurring lipoproteins can be used, such as acetylated LDL. These lipoproteins can target the delivery of polynucleotides to cells expressing lipoprotein receptors. Preferably, if lipoproteins are including with the polynucleotide to be delivered, no other targeting ligand is included in the composition.

Naturally occurring lipoproteins comprise a lipid and a protein portion. The protein portion are known as apoproteins. At the present, apoproteins A, B, C, D, and E have been isolated and identified. At least two of these contain several proteins, designated by Roman numerals, AI, AII, AIV; CI, CII, CIII.

A lipoprotein can comprise more than one apoprotein. For example, naturally occurring chylomicrons comprises of A, B, C &amp; E, over time these lipoproteins lose A and acquire C &amp; E. VLDL comprises A, B, C &amp; E apoproteins, LDL comprises apoprotein B; and HDL comprises apoproteins A, C, &amp; E.

The amino acid of these apoproteins are known and are described in, for example, Breslow (1985) <i>Annu Rev. Biochem </i>54:699; Law (1986) <i>Adv. Exp Med. Biol. </i>151:162; Chen (1986) <i>J Biol Chem </i>261:12918; Kane (1980) <i>Proc Natl Acad Sci USA </i>77:2465; and Utermann (1984) <i>Hum Genet </i>65:232.

Lipoproteins contain a variety of lipids including, triglycerides, cholesterol (free and esters), and phospholipids. The composition of the lipids varies in naturally occurring lipoproteins. For example, chylomicrons comprise mainly triglycerides. A more detailed description of the lipid content of naturally occurring lipoproteins can be found, for example, in <i>Meth. Enzymol. </i>128 (1986). The composition of the lipids are chosen to aid in conformation of the apoprotein for receptor binding activity. The composition of lipids can also be chosen to facilitate hydrophobic interaction and association with the polynucleotide binding molecule.

Naturally occurring lipoproteins can be isolated from serum by ultracentrifugation, for instance. Such methods are described in <i>Meth. Enzymol</i>. (supra); Pitas (1980) <i>J. Biochem. </i>255:5454-5460 and Mahey (1979) <i>J. Clin. Invest </i>64:743-750. Lipoproteins can also be produced by in vitro or recombinant methods by expression of the apoprotein genes in a desired host cell. See, for example, Atkinson (1986) <i>Annu Rev Biophys Chem </i>15:403 and Radding (1958) <i>Biochim Biophys Acta </i>30: 443. Lipoproteins can also be purchased from commercial suppliers, such as Biomedical Techniologies, Inc., Stoughton, Mass., USA. Further description of lipoproteins can be found in WO98/06437.

F. Polycationic Agents

Polycationic agents can be included, with or without lipoprotein, in a composition with the desired polynucleotide/polypeptide to be delivered.

Polycationic agents, typically, exhibit a net positive charge at physiological relevant pH and are capable of neutralizing the electrical charge of nucleic acids to facilitate delivery to a desired location. These agents have both in vitro, ex vivo, and in vivo applications. Polycationic agents can be used to deliver nucleic acids to a living subject either intramuscularly, subcutaneously, etc.

The following are examples of useful polypeptides as polycationic agents: polylysine, polyarginine, polyornithine, and protamine. Other examples include histones, protamines, human serum albumin, DNA binding proteins, non-histone chromosomal proteins, coat proteins from DNA viruses, such as (X174, transcriptional factors also contain domains that bind DNA and therefore may be useful as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, c-jun, c-fos, AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIID contain basic domains that bind DNA sequences.

Organic polycationic agents include: spermine, spermidine, and purtrescine.

The dimensions and of the physical properties of a polycationic agent can be extrapolated from the list above, to construct other polypeptide polycationic agents or to produce synthetic polycationic agents.

Synthetic polycationic agents which are useful include, for example, DEAE-dextran, polybrene. Lipofectin™, and lipofectAMINE™ are monomers that form polycationic complexes when combined with polynucleotides/polypeptides.

Immunodiagnostic Assays

<i>Streptococcus </i>antigens of the invention can be used in immunoassays to detect antibody levels (or, conversely, anti-<i>streptococcus </i>antibodies can be used to detect antigen levels). Immunoassays based on well defined, recombinant antigens can be developed to replace invasive diagnostics methods. Antibodies to <i>streptococcus </i>proteins within biological samples, including for example, blood or serum samples, can be detected. Design of the immunoassays is subject to a great deal of variation, and a variety of these are known in the art. Protocols for the immunoassay may be based, for example, upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use solid supports, or may be by immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide; the labels may be, for example, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the probe are also known; examples of which are assays which utilize biotin and avidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.

Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed by packaging the appropriate materials, including the compositions of the invention, in suitable containers, along with the remaining reagents and materials (for example, suitable buffers, salt solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.

Nucleic Acid Hybridisation

“Hybridization” refers to the association of two nucleic acid sequences to one another by hydrogen bonding. Typically, one sequence will be fixed to a solid support and the other will be free in solution. Then, the two sequences will be placed in contact with one another under conditions that favor hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase sequence to the solid support (Denhardt's reagent or BLOTTO); concentration of the sequences; use of compounds to increase the rate of association of sequences (dextran sulfate or polyethylene glycol); and the stringency of the washing conditions following hybridization. See Sambrook et al. [supra] Volume 2, chapter 9, pages 9.47 to 9.57.

“Stringency” refers to conditions in a hybridization reaction that favor association of very similar sequences over sequences that differ. For example, the combination of temperature and salt concentration should be chosen that is approximately 120 to 200° C. below the calculated Tm of the hybrid under study. The temperature and salt conditions can often be determined empirically in preliminary experiments in which samples of genomic DNA immobilized on filters are hybridized to the sequence of interest and then washed under conditions of different stringencies. See Sambrook et al. at page 9.50.

Variables to consider when performing, for example, a Southern blot are (1) the complexity of the DNA being blotted and (2) the homology between the probe and the sequences being detected. The total amount of the fragment(s) to be studied can vary a magnitude of 10, from 0.1 to 1 μg for a plasmid or phage digest to 10⁻⁹to 10⁻⁸g for a single copy gene in a highly complex eukaryotic genome. For lower complexity polynucleotides, substantially shorter blotting, hybridization, and exposure times, a smaller amount of starting polynucleotides, and lower specific activity of probes can be used. For example, a single-copy yeast gene can be detected with an exposure time of only 1 hour starting with 1 μg of yeast DNA, blotting for two hours, and hybridizing for 4-8 hours with a probe of 10⁸cpm/μg. For a single-copy mammalian gene a conservative approach would start with 10 μg of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfate using a probe of greater than 10⁸cpm/μg, resulting in an exposure time of −24 hours.

Several factors can affect the melting temperature (Tm) of a DNA-DNA hybrid between the probe and the fragment of interest, and consequently, the appropriate conditions for hybridization and washing. In many cases the probe is not 100% homologous to the fragment. Other commonly encountered variables include the length and total G+C content of the hybridizing sequences and the ionic strength and formamide content of the hybridization buffer. The effects of all of these factors can be approximated by a single equation: <br /><i>Tm</i>=81+16.6(log₁₀<i>Ci</i>)+0.4[%(<i>G+C</i>)]−0.6(% formamide)−600<i>/n−</i>1.5(% mismatch).<br /> where Ci is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs (slightly modified from Meinkoth &amp; Wahl (1984) <i>Anal. Biochem. </i>138: 267-284).

In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be conveniently altered. The temperature of the hybridization and washes and the salt concentration during the washes are the simplest to adjust. As the temperature of the hybridization increases (ie. stringency), it becomes less likely for hybridization to occur between strands that are nonhomologous, and as a result, background decreases. If the radiolabeled probe is not completely homologous with the immobilized fragment (as is frequently the case in gene family and interspecies hybridization experiments), the hybridization temperature must be reduced, and background will increase. The temperature of the washes affects the intensity of the hybridizing band and the degree of background in a similar manner. The stringency of the washes is also increased with decreasing salt concentrations.

In general, convenient hybridization temperatures in the presence of 50% formamide are 42° C. for a probe with is 95% to 100% homologous to the target fragment, 37° C. for 90% to 95% homology, and 32° C. for 85% to 90% homology. For lower homologies, formamide content should be lowered and temperature adjusted accordingly, using the equation above. If the homology between the probe and the target fragment are not known, the simplest approach is to start with both hybridization and wash conditions which are nonstringent. If non-specific bands or high background are observed after autoradiography, the filter can be washed at high stringency and reexposed. If the time required for exposure makes this approach impractical, several hybridization and/or washing stringencies should be tested in parallel.

Nucleic Acid Probe Assays

Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid probes according to the invention can determine the presence of cDNA or mRNA. A probe is said to “hybridize” with a sequence of the invention if it can form a duplex or double stranded complex, which is stable enough to be detected.

The nucleic acid probes will hybridize to the <i>streptococcus </i>nucleotide sequences of the invention (including both sense and antisense strands). Though many different nucleotide sequences will encode the amino acid sequence, the native <i>streptococcus </i>sequence is preferred because it is the actual sequence present in cells. mRNA represents a coding sequence and so a probe should be complementary to the coding sequence; single-stranded cDNA is complementary to mRNA, and so a cDNA probe should be complementary to the non-coding sequence.

The probe sequence need not be identical to the <i>streptococcus </i>sequence (or its complement)—some variation in the sequence and length can lead to increased assay sensitivity if the nucleic acid probe can form a duplex with target nucleotides, which can be detected. Also, the nucleic acid probe can include additional nucleotides to stabilize the formed duplex. Additional <i>streptococcus </i>sequence may also be helpful as a label to detect the formed duplex. For example, a non-complementary nucleotide sequence may be attached to the 5′ end of the probe, with the remainder of the probe sequence being complementary to a <i>streptococcus </i>sequence. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the a <i>streptococcus </i>sequence in order to hybridize therewith and thereby form a duplex which can be detected.

The exact length and sequence of the probe will depend on the hybridization conditions (e.g. temperature, salt condition etc.). For example, for diagnostic applications, depending on the complexity of the analyte sequence, the nucleic acid probe typically contains at least 10-20 nucleotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be shorter than this. Short primers generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.

Probes may be produced by synthetic procedures, such as the triester method of Matteucci et al. [<i>J. Am. Chem. Soc</i>. (1981) 103:3185], or according to Urdea et al. [<i>Proc. Natl. Acad. Sci. USA </i>(1983) 80: 7461], or using commercially available automated oligonucleotide synthesizers.

The chemical nature of the probe can be selected according to preference. For certain applications, DNA or RNA are appropriate. For other applications, modifications may be incorporated eg. backbone modifications, such as phosphorothioates or methylphosphonates, can be used to increase in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see Agrawal &amp; Iyer (1995) <i>Curr Opin Biotechnol </i>6:12-19; Agrawal (1996) <i>TIBTECH </i>14:376-387]; analogues such as peptide nucleic acids may also be used [eg. see Corey (1997) <i>TIBTECH </i>15:224-229; Buchardt et al. (1993) <i>TIBTECH </i>11:384-386].

Alternatively, the polymerase chain reaction (PCR) is another well-known means for detecting small amounts of target nucleic acid. The assay is described in Mullis et al. [<i>Meth. Enzymol</i>. (1987) 155:335-350] &amp; U.S. Pat. Nos. 4,683,195 &amp; 4,683,202. Two “primer” nucleotides hybridize with the target nucleic acids and are used to prime the reaction. The primers can comprise sequence that does not hybridize to the sequence of the amplification target (or its complement) to aid with duplex stability or, for example, to incorporate a convenient restriction site. Typically, such sequence will flank the desired <i>streptococcus </i>sequence.

A thermostable polymerase creates copies of target nucleic acids from the primers using the original target nucleic acids as a template. After a threshold amount of target nucleic acids are generated by the polymerase, they can be detected by more traditional methods, such as Southern blots. When using the Southern blot method, the labelled probe will hybridize to the <i>streptococcus </i>sequence (or its complement).

Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook et al [supra]. mRNA, or cDNA generated from mRNA using a polymerase enzyme, can be purified and separated using gel electrophoresis. The nucleic acids on the gel are then blotted onto a solid support, such as nitrocellulose. The solid support is exposed to a labelled probe and then washed to remove any unhybridized probe. Next, the duplexes containing the labeled probe are detected. Typically, the probe is labelled with a radioactive moiety.

BRIEF DESCRIPTION OF DRAWINGS

<figref idrefs="DRAWINGS">FIGS. 1 to 85</figref>, <b>119</b> to <b>188</b>, <b>238</b> and <b>239</b> show SDS-PAGE analysis of total cell extracts from cultures of recombinant <i>E. coli </i>expressing GBS proteins of the invention. Lane 1 in each gel (except for <figref idrefs="DRAWINGS">FIG. 185</figref>) contains molecular weight markers. These are 94, 67, 43, 30, 20.1 &amp; 14.4 kDa (except for <figref idrefs="DRAWINGS">FIGS. 7</figref>, <b>8</b>, <b>10</b>, <b>11</b>, <b>13</b>, <b>14</b>, <b>15</b> and <b>119</b>-<b>170</b>, which use 250, 150, 100, 75, 50, 37, 25, 15 &amp; 10 kDa).

<figref idrefs="DRAWINGS">FIG. 86A</figref> shows the pDEST15 vector and <figref idrefs="DRAWINGS">FIG. 86B</figref> shows the pDEST17-1 vector.

<figref idrefs="DRAWINGS">FIGS. 88 to 118</figref> and <b>247</b> to <b>319</b> show protein characterisation data for various proteins of the invention.

<figref idrefs="DRAWINGS">FIGS. 189 to 237</figref> and <b>240</b> to <b>246</b> show SDS-PAGE analysis of purified GBS proteins of the invention. The left-hand lane contains molecular weight markers. These are 94, 67, 43, 30, 20.1 &amp; 14.4 kDa.

MODES FOR CARRYING OUT THE INVENTION

The following examples describe nucleic acid sequences which have been identified in <i>Streptococcus</i>, along with their inferred translation products. The examples are generally in the following format: <ul><li id="ul0003-0001" num="0000"><ul><li id="ul0004-0001" num="0240">a nucleotide sequence which has been identified in <i>Streptococcus </i></li><li id="ul0004-0002" num="0241">the inferred translation product of this sequence</li><li id="ul0004-0003" num="0242">a computer analysis (e.g. PSORT output) of the translation product, indicating antigenicity</li></ul></li></ul>

Most examples describe nucleotide sequences from <i>S. agalactiae</i>. The specific strain which was sequenced was from serotype V, and is a clinical strain isolated in Italy which expresses the R antigen (ISS/Rome/Italy collection, strain.2603 V/R). For several of these examples, the corresponding sequences from <i>S. pyogenes </i>are also given. Where GBS and GAS show homology in this way, there is conservation between species which suggests an essential function and also gives good cross-species reactivity.

In contrast, several examples describe nucleotide sequences from GAS for which no homolog in GBS has been identified. This lack of homology gives molecules which are useful for distinguishing GAS from GBS and for making GAS-specific products. The same is true for GBS sequences which lack GAS homologs e.g. these are useful for making GBS-specific products.

The examples typically include details of homology to sequences in the public databases. Proteins that are similar in sequence are generally similar in both structure and function, and the homology often indicates a common evolutionary origin. Comparison with sequences of proteins of known function is widely used as a guide for the assignment of putative protein function to a new sequence and has proved particularly useful in whole-genome analyses.

Various tests can be used to assess the in vivo immunogenicity of the proteins identified in the examples. For example, the proteins can be expressed recombinantly and used to screen patient sera by immunoblot. A positive reaction between the protein and patient serum indicates that the patient has previously mounted an immune response to the protein in question i.e. the protein is an immunogen. This method can also be used to identify immunodominant proteins. The mouse model used in the examples can also be used.

The recombinant protein can also be conveniently used to prepare antibodies e.g. in a mouse. These can be used for direct confirmation that a protein is located on the cell-surface. Labelled antibody (e.g. fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label on the bacterial surface confirms the location of the protein.

For many GBS proteins, the following data are given: <ul><li id="ul0005-0001" num="0000"><ul><li id="ul0006-0001" num="0249">SDS-PAGE analysis of total recombinant <i>E. coli </i>cell extracts for GBS protein expression</li><li id="ul0006-0002" num="0250">SDS-PAGE analysis after the protein purification</li><li id="ul0006-0003" num="0251">Western-blot analysis of GBS total cell extract using antisera raised against recombinant proteins</li><li id="ul0006-0004" num="0252">FACS and ELISA analysis against GBS using antisera raise against recombinant proteins</li><li id="ul0006-0005" num="0253">Results of the in vivo passive protection assay</li></ul></li></ul>

Details of experimental techniques used are presented below:

Sequence Analysis

Open reading frames (ORFs) within nucleotide sequences were predicted using the GLIMMER program [Salzberg et al. (1998) <i>Nucleic Acids Res </i>26:544-8]. Where necessary, start codons were modified and corrected manually on the basis of the presence of ribosome-binding sites and promoter regions on the upstream DNA sequence.

ORFs were then screened against the non-redundant protein databases using the programs BLASTp [Altschul et al. (1990) <i>J. Mol. Biol. </i>215:403-410] and PRAZE, a modification of the Smith-Waterman algorithm [Smith &amp; Waterman (1981) <i>J Mol Biol </i>147:195-7; see Fleischmann et al (1995) <i>Science </i>269:496-512].

Leader peptides within the ORFs were located using three different approaches: (i) PSORT [Nakai (1991) <i>Bull. Inst. Chem. Res., Kyoto Univ. </i>69:269-291; Horton &amp; Nakai (1996) <i>Intellig. Syst. Mol. Biol. </i>4:109-115; Horton &amp; Nakai (1997) <i>Intellig. Syst. Mol. Biol. </i>5:147-152]; (ii) SignalP [Nielsen &amp; Krogh (1998) in <i>Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology </i>(<i>ISMB </i>6), AAAI Press, Menlo Park, Calif., pp. 122-130; Nielsen et al. (1999) <i>Protein Engineering </i>12:3-9; Nielsen et al. (1997). <i>Int. J. Neural Sys. </i>8:581-599]; and (iii) visual inspection of the ORF sequences. Where a signal sequences is given a “possible site” value, the value represents the C-terminus residue of the signal peptide e.g. a “possible site” of 26 means that the signal sequence consists of amino acids 1-26.

Lipoprotein-specific signal peptides were located using three different approaches: (i) PSORT [see above]; (ii) the “prokaryotic membrane lipoprotein lipid attachment site” PROSITE motif [Hofmann et al. (1999) <i>Nucleic Acids Res. </i>27:215-219; Bucher &amp; Bairoch (1994) in <i>Proceedings </i>2<i>nd International Conference on Intelligent Systems for Molecular Biology </i>(ISMB-94), AAAI Press, pages 53-61]; and (iii) the FINDPATTERNS program available in the GCG Wisconsin Package, using the pattern (M, L, V)x{9, 35} LxxCx.

Transmembrane domains were located using two approaches: (i) PSORT [see above]; (ii) TopPred [von Heijne (1992) <i>J. Mol. Biol. </i>225:487-494].

LPXTG motifs, characteristic of cell-wall attached proteins in Gram-positive bacteria [Fischetti et al. (1990) <i>Mol Microbiol </i>4:1603-5] were located, with FINDPATTERNS using the pattern (L, I, V, M, Y, F)Px(T, A, S, G)(G, N, S, T, A, L).

RGD motifs, characteristic of cell-adhesion molecules [D'Souza et al. (1991) <i>Trends Biochem Sci </i>16:246-50] were located using FINDPATTERNS.

Enzymes belonging to the glycolytic pathway were also selected as antigens, because these have been found experimentally expressed on the surface of Streptococci [e.g. Pancholi &amp; Fischetti (1992) <i>J Exp Med </i>176:415-26; Pancholi &amp; Fischetti (1998) <i>J Biol Chem </i>273:14503-15].

Cloning, Expression and Purification of Proteins

GBS genes were cloned to facilitate expression in <i>E. coli </i>as two different types of fusion proteins: <ul><li id="ul0007-0001" num="0000"><ul><li id="ul0008-0001" num="0264">a) proteins having a hexa-histidine tag at the amino-terminus (His-gbs)</li><li id="ul0008-0002" num="0265">b) proteins having a GST fusion partner at the amino-terminus (Gst-gbs)</li></ul></li></ul>

Cloning was performed using the Gateway™ technology (Life Technologies), which is based on the site-specific recombination reactions that mediate integration and excision of phage lambda into and from the <i>E. coli </i>genome. A single cloning experiment included the following steps: <ul><li id="ul0009-0001" num="0000"><ul><li id="ul0010-0001" num="0267">1—Amplification of GBS chromosomal DNA to obtain a PCR product coding for a single ORF flanked by attB recombination sites. </li><li id="ul0010-0002" num="0268">2—Insertion of the PCR product into a pDONR vector (containing attP sites) through a BP reaction (attB×attP sites). This reaction gives a so called ‘pEntry’ vector, which now contains attL sites flanking the insert.</li><li id="ul0010-0003" num="0269">3—Insertion of the GBS gene into <i>E. coli </i>expression vectors (pDestination vectors, containing attR sites) through a LR reaction between pEntry and pDestination plasmids (attL×attR sites). <br /> A) Chromosomal DNA Preparation </li></ul></li></ul>

For chromosomal DNA preparation, GBS strain 2603 V/R (Istituto Superiore Sanita, Rome) was grown to exponential phase in 2 liters TH Broth (Difco) at 37° C., harvested by centrifugation, and dissolved in 40 ml TES (50 mM Tris pH 8, 5 mM EDTA pH 8, 20% sucrose). After addition of 2.5 ml lysozyme solution (25 mg/ml in TES) and 0.5 ml mutanolysin (Sigma M-9901, 25000 U/ml in H₂O), the suspension was incubated at 37° C. for 1 hour. 1 ml RNase (20 mg/ml) and 0.1 ml proteinase K (20 mg/ml) were added and incubation was continued for 30 min. at 37° C.

Cell lysis was obtained by adding 5 ml sarkosyl solution (10% N-laurylsarcosine in 250 mM EDTA pH 8.0), and incubating 1 hour at 37° C. with frequent inversion. After sequential extraction with phenol, phenol-chloroform and chloroform, DNA was precipitated with 0.3M sodium acetate pH 5.2 and 2 volumes of absolute ethanol. The DNA pellet was rinsed with 70% ethanol and dissolved in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). DNA concentration was evaluated by OD₂₆₀.

B) Oligonucleotide Design

Synthetic oligonucleotide primers were designed on the basis of the coding sequence of each ORF. The aim was to express the protein's extracellular region. Accordingly, predicted signal peptides were omitted (by deducing the 5′ end amplification primer sequence immediately downstream from the predicted leader sequence) and C-terminal cell-wall ancoring regions were removed (e.g. LPXTG motifs and downstream amino acids). Where additional nucleotides have been deleted, this is indicated by the suffix ‘d’ (e.g. ‘GBS352d’—see Table V). Conversely, a suffix ‘L’ refers to expression without these deletions. Deletions of C- or N-terminal residues were also sometimes made, as indicated by a ‘C’ or ‘N’ suffix.

The amino acid sequences of the expressed GBS proteins (including ‘d’ and ‘L’ forms etc.) are definitively defined by the sequences of the oligonuclotides primers given in Table II.

5′ tails of forward primers and 3′ tails of reverse primers included attB1 and attB2 sites respectively: <ul><li id="ul0011-0001" num="0275">Forward primers: 5′-GGGGACAAGTTTGTACAAAAAAGCAGGCTCT-ORF in frame-3′ (the TCT sequence preceding the ORF was omitted when the ORF's first coding triplet began with T). </li><li id="ul0011-0002" num="0276">Reverse primers: 5′-GGGGACCACTTTGTACAAGAAAGCTGGGTT-ORF reverse complement-3′.</li></ul>

The number of nucleotides which hybridized to the sequence to be amplified depended on the melting temperature of the primers, which was determined as described by Breslauer et al. [<i>PNAS USA </i>(1986) 83:3746-50]. The average melting temperature of the selected oligos was 50-55° C. for the hybridizing region and 80-85° C. for the whole oligos.

C) Amplification

The standard PCR protocol was as follows: 50 ng genomic DNA were used as template in the presence of 0.5 μM each primer, 200 μM each dNTP, 1.5 mM MgCl₂, 1× buffer minus Mg⁺⁺ (Gibco-BRL) and 2 units of Taq DNA polymerase (Platinum Taq, Gibco-BRL) in a final volume of 100 μl. Each sample underwent a double-step of amplification: 5 cycles performed using as the hybridizing temperature 50° C., followed by 25 cycles at 68° C.

The standard cycles were as follows:

<tables id="TABLE-US-00001" num="00001"><table frame="none" colsep="0" rowsep="0"><tgroup align="left" colsep="0" rowsep="0" cols="3"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="42pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><thead><row><entry /><entry namest="offset" nameend="2" align="center" rowsep="1" /></row></thead><tbody valign="top"><row><entry /><entry /><entry>Denaturation: 94° C., 2 min</entry></row><row><entry /><entry> 5 cycles:</entry><entry>Denaturation: 94° C., 30 seconds</entry></row><row><entry /><entry /><entry>Hybridization: 50° C., 50 seconds</entry></row><row><entry /><entry /><entry>Elongation: 72° C., 1 min. or 2 min. and 40 sec.</entry></row><row><entry /><entry>25 cycles:</entry><entry>Denaturation: 94° C., 30 seconds</entry></row><row><entry /><entry /><entry>Hybridization: 68° C., 50 seconds</entry></row><row><entry /><entry /><entry>Elongation: 72° C., 1 min. or 2 min. and 40 sec.</entry></row><row><entry /><entry namest="offset" nameend="2" align="center" rowsep="1" /></row></tbody></tgroup></table></tables>

Elongation time was 1 minute for ORFs shorter than 2000 bp and 2:40 minutes for ORFs longer than 2000 bp. Amplifications were performed using a Gene Amp PCR system 9600 (Perkin Elmer).

To check amplification results, 2 μl of each PCR product were loaded onto 1-1.5 agarose gel and the size of amplified fragments was compared with DNA molecular weight standards (DNA marker IX Roche, 1 kb DNA ladder Biolabs).

Single band PCR products were purified by PEG precipitation: 300 μl of TE buffer and 200 μl of 30% PEG 8000/30 mM MgCl₂were added to 100 μl PCR reaction. After vortexing, the DNA was centrifuged for 20 min at 10000 g, washed with 1 vol. 70% ethanol and the pellet dissolved in 30 μl TE. PCR products smaller than 350 bp were purified using a PCR purification Kit (Qiagen) and eluted with 30 μl of the provided elution buffer.

In order to evaluate the yield, 2 μl of the purified DNA were subjected to agarose gel electrophoresis and compared to titrated molecular weight standards.

D) Cloning of PCR Products into Expression Vectors

Cloning was performed following the Gateway™ technology's “one-tube protocol”, which consists of a two step reaction (BP and LR) for direct insertion of PCR products into expression vectors.

BP reaction (attB×attP sites): The reaction allowed insertion of the PCR product into a pDONR vector. The pDONR™ 201 vector we used contains the killer toxin gene ccdB between attP1 and attP2 sites to minimize background colonies lacking the PCR insert, and a selectable marker gene for kanamycin resistance. The reaction resulted in a so called pEntry vector, in which the GBS gene was located between attL1 and attL2 sites.

60 fmol of PCR product and 100 ng of pDONR™ 201 vector were incubated with 2.5 μl of BP Clonase™ in a final volume of 12.5 μl for 4 hours at 25° C.

LR reaction (attL×attR sites): The reaction allowed the insertion of the GBS gene, now present in the pEntry vector, into <i>E. coli </i>expression vectors (pDestination vectors, containing attR sites). Two pDestination vectors were used (PDEST15 for N-terminal GST fusions—<figref idrefs="DRAWINGS">FIG. 86</figref>; and pDEST17-1 for N-terminal His-tagged fusions—<figref idrefs="DRAWINGS">FIG. 87</figref>). Both allow transcription of the ORF fusion coding mRNA under T7 RNA polymerase promoter [Studier et al (1990) <i>Meth. Enzymol </i>185: 60ff].

To 5 μl of BP reaction were added 0.25 μl of 0.75 M NaCl, 100 ng of destination vector and 1.5 μl of LR Clonase™. The reaction was incubated at 25° C. for 2 hours and stopped with 1 μl of 1 mg/ml proteinase K solution at 37° C. for 15 min.

1 μl of the completed reaction was used to transform 50 μl electrocompetent BL21-SI™ cells (0.1 cm, 200 ohms, 25 μF). BL21-SI cells contain an integrated T7 RNA polymerase gene under the control of the salt-inducible prU promoter [Gowrishankar (1985) <i>J. Bacteriol. </i>164:434ff]. After electroporation cells were diluted in 1 ml SOC medium (20 g/l bacto-tryptone, 5 g/l yeast extract, 0.58 g/l NaCl, 0.186 g/l KCl, 20 mM glucose, 10 mM MgCl₂) and incubated at 37° C. for 1 hour. 200 μl cells were plated onto LBON plates (Luria Broth medium without NaCl) containing 100 μg/ml ampicillin. Plates were then incubated for 16 hours at 37° C.

Entry clones: In order to allow the future preparation of Gateway compatible pEntry plasmids containing genes which might turn out of interest after immunological assays, 2.5 μl of BP reaction were incubated for 15 min in the presence of 3 μl 0.15 mg/ml proteinase K solution and then kept at −20° C. The reaction was in this way available to transform <i>E. coli </i>competent cells so as to produce Entry clones for future introduction of the genes in other Destination vectors. <br /> E) Protein Expression

Single colonies derived from the transformation of LR reactions were inoculated as small-scale cultures in 3 ml LBON 100 μg/ml ampicillin for overnight growth at 25° C. 50-200 μl of the culture was inoculated in 3 ml LBON/Amp to an initial OD600 of 0.1. The cultures were grown at 37° C. until OD600 0.4-0.6 and recombinant protein expression was induced by adding NaCl to a final concentration of 0.3 M. After 2 hour incubation the final OD was checked and the cultures were cooled on ice. 0.5 OD₆₀₀of cells were harvested by centrifugation. The cell pellet was suspended in 50 μl of protein Loading Sample Buffer (50 mM TRIS-HCl pH 6.8, 0.5% w/v SDS, 2.5% v/v glycerin, 0.05% w/v Bromophenol Blue, 100 mM DTT) and incubated at 100 IC for 5 min. 10 μl of sample was analyzed by SDS-PAGE and Coomassie Blue staining to verify the presence of induced protein band.

F) Purification of the Recombinant Proteins

Single colonies were inoculated in 25 ml LBON 100 μg/ml ampicillin and grown at 25° C. overnight. The overnight culture was inoculated in 500 ml LBON/amp and grown under shaking at 25 IC until OD₆₀₀values of 0.4-0.6. Protein expression was then induced by adding NaCl to a final concentration of 0.3 M. After 3 hours incubation at 25 IC the final OD₆₀₀was checked and the cultures were cooled on ice. After centrifugation at 6000 rpm (JA10 rotor, Beckman) for 20 min., the cell pellet was processed for purification or frozen at −20° C.

Proteins were purified in 1 of 3 ways depending on the fusion partner and the protein's solubility:

Purification of Soluble His-Tagged Proteins from <i>E. coli </i>

<ul><li id="ul0012-0001" num="0000"><ul><li id="ul0013-0001" num="0295">1. Transfer pellets from −20° C. to ice bath and reconstitute each pellet with 10 ml B-PER™ solution (Bacterial-Protein Extraction Reagent, Pierce cat. 78266), 10 μl of a 100 mM MgCl₂solution, 50 μl of DNAse I (Sigma D-4263, 100 Kunits in PBS) and 100 μl of 100 mg/ml lysozyme in PBS (Sigma L-7651, final concentration 1 mg/ml).</li><li id="ul0013-0002" num="0296">2. Transfer resuspended pellets in 50 ml centrifuge tubes and leave at room temperature for 30-40 minutes, vortexing 3-4 times.</li><li id="ul0013-0003" num="0297">3. Centrifuge 15-20 minutes at about 30-40000×g.</li><li id="ul0013-0004" num="0298">4. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating Sepharose (Pharmacia). Equilibrate with 50 mM phosphate buffer, 300 mM NaCl, pH 8.0.</li><li id="ul0013-0005" num="0299">5. Store the pellet at −20° C., and load the supernatant on to the columns.</li><li id="ul0013-0006" num="0300">6. Discard the flow through.</li><li id="ul0013-0007" num="0301">7. Wash with 10 ml 20 mM imidazole buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0.</li><li id="ul0013-0008" num="0302">8. Elute the proteins bound to the columns with 4.5 ml (1.5 ml+1.5 ml+1.5 ml) 250 mM imidazole buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0 and collect three fractions of ˜1.5 ml each. Add to each tube 15 μl DTT 200 mM (final concentration 2 mM). </li><li id="ul0013-0009" num="0303">9. Measure the protein concentration of the collected fractions with the Bradford method and analyse the proteins by SDS-PAGE.</li><li id="ul0013-0010" num="0304">10. Store the collected fractions at +4° C. while waiting for the results of the SDS-PAGE analysis.</li><li id="ul0013-0011" num="0305">11. For immunisation prepare 4-5 aliquots of 20-100 μg each in 0.5 ml in 40% glycerol. The dilution buffer is the above elution buffer, plus 2 mM DTT. Store the aliquots at −20° C. until immunisation. <br /> Purification of His-Tagged Proteins from Inclusion Bodies </li><li id="ul0013-0012" num="0306">1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at −20° C. Transfer the pellets from −20° C. to room temperature and reconstitute each pellet with 10 ml B-PER™ solution, 10 μl of a 100 mM MgCl₂solution (final 1 mM), 50 μl of DNAse 1 equivalent to 100 Kunits units in PBS and 100 μl of a 100 mg/ml lysozime (Sigma L-7651) solution in PBS (equivalent to 10 mg, final concentration 1 mg/ml).</li><li id="ul0013-0013" num="0307">2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40 minutes, vortexing 3-4 times.</li><li id="ul0013-0014" num="0308">3. Centrifuge 15 minutes at 30-4000×g and collect the pellets.</li><li id="ul0013-0015" num="0309">4. Dissolve the pellets with 50 mM TRIS-HCl, 1 mM TCEP {Tris(2-carboxyethyl)-phosphine hydrochloride, Pierce}, 6M guanidine hydrochloride, pH 8.5. Stir for ˜10 min. with a magnetic bar.</li><li id="ul0013-0016" num="0310">5. Centrifuge as described above, and collect the supernatant.</li><li id="ul0013-0017" num="0311">6. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating Sepharose (Pharmacia). Wash the columns twice with 5 ml of H₂0 and equilibrate with 50 mM TRIS-HCl, 1 mM TCEP, 6M guanidine hydrochloride, pH 8.5.</li><li id="ul0013-0018" num="0312">7. Load the supernatants from step 5 onto the columns, and wash with 5 ml of 50 mM TRIS-HCl buffer, 1 mM TCEP, 6M urea, pH 8.5</li><li id="ul0013-0019" num="0313">8. Wash the columns with 10 ml of 20 mM imidazole, 50 mM TRIS-HCl, 6M urea, 1 mM TCEP, pH 8.5. Collect and set aside the first 5 ml for possible further controls.</li><li id="ul0013-0020" num="0314">9. Elute proteins bound to columns with 4.5 ml buffer containing 250 mM imidazole, 50 mM TRIS-HCl, 6M urea, 1 mM TCEP, pH 8.5. Add the elution buffer in three 1.5 ml aliquots, and collect the corresponding three fractions. Add to each fraction 15 μl DTT (final concentration 2 mM).</li><li id="ul0013-0021" num="0315">10. Measure eluted protein concentration with Bradford method and analyse proteins by SDS-PAGE. </li><li id="ul0013-0022" num="0316">11. Dialyse overnight the selected fraction against 50 mM Na phosphate buffer, pH 8.8, containing 10% glycerol, 0.5 M arginine, 5 mM reduced glutathione, 0.5 mM oxidized glutathione, 2 M urea.</li><li id="ul0013-0023" num="0317">12. Dialyse against 50 mM Na phosphate buffer, pH 8.8, containing 10% glycerol, 0.5 M arginine, 5 mM reduced glutathione, 0.5 mM oxidized glutathione.</li><li id="ul0013-0024" num="0318">13. Clarify the dialysed protein preparation by centrifugation and discard the non-soluble material and measure the protein concentration with the Bradford method.</li><li id="ul0013-0025" num="0319">14. For each protein destined to the immunization prepare 4-5 aliquot of 20-100 μg each in 0.5 ml after having adjusted the glycerol content up to 40%. Store the prepared aliquots at −20° C. until immunization. <br /> Purification of GST-Fusion Proteins from <i>E. coli </i></li><li id="ul0013-0026" num="0320">1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at −20° C. Transfer the pellets from −20° C. to room temperature and reconstitute each pellet with 10 ml B-PER™ solution, 10 μl of a 100 mM MgCl₂solution (final 1 mM), 50 μl of DNAse 1 equivalent to 100 Kunits units in PBS and 100 μl of a 100 mg/ml lysozime (Sigma L-7651) solution in PBS (equivalent to 10 mg, final concentration 1 mg/ml).</li><li id="ul0013-0027" num="0321">2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40 minutes, vortexing 3-4 times.</li><li id="ul0013-0028" num="0322">3. Centrifuge 15-20 minutes at about 30-40000×g.</li><li id="ul0013-0029" num="0323">4. Discard centrifugation pellets and load supernatants onto the chromatography columns, as follows.</li><li id="ul0013-0030" num="0324">5. Prepare Poly-Prep (Bio-Rad) columns containing 0.5 ml of Glutathione-Sepharose 4B resin. Wash the columns twice with 1 ml of H₂O and equilibrate with 10 ml PBS, pH 7.4.</li><li id="ul0013-0031" num="0325">6. Load supernatants on to the columns and discard the flow through.</li><li id="ul0013-0032" num="0326">7. Wash the columns with 10 ml PBS, pH 7.4.</li><li id="ul0013-0033" num="0327">8. Elute proteins bound to columns with 4.5 ml of 50 mM TRIS buffer, 10 mM reduced glutathione, pH 8.0, adding 1.5 ml+1.5 ml+1.5 ml and collecting the respective 3 fractions of ˜1.5 ml each.</li><li id="ul0013-0034" num="0328">9. Measure protein concentration of the fractions with the Bradford method and analyse the proteins by SDS-PAGE.</li><li id="ul0013-0035" num="0329">10. Store the collected fractions at +4° C. while waiting for the results of the SDS-PAGE analysis. </li><li id="ul0013-0036" num="0330">11. For each protein destined for immunisation prepare 4-5 aliquots of 20-100 μg each in 0.5 ml of 40% glycerol. The dilution buffer is 50 mM TRIS-HCl, 2 mM DTT, pH 8.0. Store the aliquots at −20° C. until immunisation. <br /><figref idrefs="DRAWINGS">FIGS. 167 to 170</figref> and <b>238</b> to <b>239</b></li></ul></li></ul>

For the experiments shown in <figref idrefs="DRAWINGS">FIGS. 167 to 170</figref>, <figref idrefs="DRAWINGS">FIG. 238</figref> and lanes 2-6 of <figref idrefs="DRAWINGS">FIG. 239</figref>, the GBS proteins were fused at the N-terminus to thioredoxin and at C-terminus to a poly-His tail. The plasmid used for cloning is pBAD-DEST49 (Invitrogen Gateway™ technology) and expression is under the control of an L(+)-Arabinose dependent promoter. For the production of these GBS antigens, bacteria are grown on RM medium (6 g/l Na₂HPO₄, 3 g/l KH₂PO₄, 0.5 g/l NaCl, 1 g/l NH₄Cl, pH7.4, 2% casaminoacids, 0.2% glucose, 1 mM MgCl₂) containing 100 μg/ml ampicillin. After incubation at 37° C. until cells reach OD₆₀₀=0.5, protein expression is induced by adding 0.2% (v/v) L(+)Arabinose for 3 hours.

Immunisations with GBS Proteins

The purified proteins were used to immunise groups of four CD-1 mice intraperitoneally. 20 μg of each purified protein was injected in Freund's adjuvant at days 1, 21 &amp; 35. Immune responses were monitored by using samples taken on day 0 &amp; 49. Sera were analysed as pools of sera from each group of mice.

FACScan Bacteria Binding Assay Procedure.

GBS serotype V 2603 V/R strain was plated on TSA blood agar plates and incubated overnight at 37° C. Bacterial colonies were collected from the plates using a sterile dracon swab and inoculated into 100 ml Todd Hewitt Broth. Bacterial growth was monitored every 30 minutes by following OD₆₀₀. Bacteria were grown until OD₆₀₀=0.7-0.8. The culture was centrifuged for 20 minutes at 5000 rpm. The supernatant was discarded and bacteria were washed once with PBS, resuspended in ½ culture volume of PBS containing 0.05% paraformaldehyde, and incubated for 1 hour at 37° C. and then overnight at 4° C.

50 μl bacterial cells (OD₆₀₀0.1) were washed once with PBS and resuspended in 20 μl blocking serum (Newborn Calf Serum, Sigma) and incubated for 20 minutes at room temperature. The cells were then incubated with 100 μl diluted sera (1:200) in dilution buffer (20% Newborn Calf Serum 0.1% BSA in PBS) for 1 hour at 4° C. Cells were centrifuged at 5000 rpm, the supernatant aspirated and cells washed by adding 200 μl washing buffer (0.1% BSA in PBS). 50 μl R-Phicoerytrin conjugated F(ab)₂goat anti-mouse, diluted 1:100 in dilution buffer, was added to each sample and incubated for 1 hour at 4° C. Cells were spun down by centrifugation at 5000 rpm and washed by adding 200 μl of washing buffer. The supernatant was aspirated and cells resuspended in 200 μl PBS. Samples were transferred to FACScan tubes and read. The condition for FACScan setting were: FL2 on; FSC-H threshold:54; FSC PMT Voltage: E 02; SSC PMT: 516; Amp. Gains 2.63; FL-2 PMT: 728. Compensation values: 0.

Samples were considered as positive if they had a Δ mean values&gt;50 channel values.

Whole Extracts Preparation

GBS serotype III COH1 strain and serotype V 2603 V/R strain cells were grown overnight in Todd Hewitt Broth. 1 ml of the culture was inoculated into 100 ml Todd Hewitt Broth. Bacterial growth was monitored every 30 minutes by following OD₆₀₀. The bacteria were grown until the OD reached 0.7-0.8. The culture was centrifuged for 20 minutes at 5000 rpm. The supernatant was discarded and bacteria were washed once with PBS, resuspended in 2 ml 50 mM Tris-HCl, pH 6.8 adding 400 units of Mutanolysin (Sigma-Aldrich) and incubated 3 hrs at 37° C. After 3 cycles of freeze/thaw, cellular debris were removed by centrifugation at 14000 g for 15 minutes and the protein concentration of the supernatant was measured by the Bio-Rad Protein assay, using BSA as a standard.

Western Blotting

Purified proteins (50 ng) and total cell extracts (25 μg) derived from GBS serotype III COH1 strain and serotype V 2603 V/R strain were loaded on 12% or 15% SDS-PAGE and transferred to a nitrocellulose membrane. The transfer was performed for 1 hours at 100V at 4° C., in transferring buffer (25 mM Tris base, 192 mM glycine, 20% methanol). The membrane was saturated by overnight incubation at 4° C. in saturation buffer (5% skimmed milk, 0.1% Tween 20 in PBS). The membrane was incubated for 1 hour at room temperature with 1:1000 mouse sera diluted in saturation buffer. The membrane was washed twice with washing buffer (3% skimmed milk, 0.1% Tween 20 in PBS) and incubated for 1 hour with a 1:5000 dilution of horseradish peroxidase labelled anti-mouse Ig (Bio-Rad). The membrane was washed twice with 0.1% Tween 20 in PBS and developed with the Opti-4CN Substrate Kit (Bio-Rad). The reaction was stopped by adding water.

Unless otherwise indicated, lanes 1, 2 and 3 of blots in the drawings are: (1) the purified protein; (2) GBS-III extracts; and (3) GBS-V extracts. Molecular weight markers are also shown.

In Vivo Passive Protection Assay in Neonatal Sepsis Mouse model.

The immune sera collected from the CD1 immunized mice were tested in a mouse neonatal sepsis model to verify their protective efficacy in mice challenged with GBS serotype III. Newborn Balb/C littermates were randomly divided in two groups within 24 hrs from birth and injected subcutaneously with 25 μl of diluted sera (1:15) from immunized CD1 adult mice. One group received preimmune sera, the other received immune sera. Four hours later all pups were challenged with a 75% lethal dose of the GBS serotype III COH1 strain. The challenge dose obtained diluting a mid log phase culture was administered subcutaneously in 25 μl of saline. The number of pups surviving GBS infection was assessed every 12 hours for 4 days. Results are in Table III.

EXAMPLE 1

A DNA sequence (GBSx1402) was identified in <i>S. agalactiae </i>&lt;SEQ ID I&gt; which encodes the amino acid sequence &lt;SEQ ID 2&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00002" num="00002"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="42pt" align="left" /><colspec colname="5" colwidth="56pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −0.48</entry><entry>Transmembrane</entry><entry>169-185</entry><entry>(169-185)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1192 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database.

<tables id="TABLE-US-00003" num="00003"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB88235 GB: AL353012 hypothetical serine-rich repeat protein</entry><entry /></row><row><entry>[<i>Schizosaccharomyces pombe</i>]</entry></row><row><entry>Identities = 41/152 (26%), Positives = 75/152 (48%), Gaps = 4/152 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>22</entry><entry>SSIGYADTSDKNTDTSVVTTTLSEEKRSDELDQSSTGSSSENESSSSSEPETNPSTNPPT</entry><entry>81</entry><entry /></row><row><entry /><entry /><entry>SS   +++S +++D+S  ++    E  S+  D SS+ SSSE+ESSS     ++ S++  +</entry></row><row><entry>Sbjct:</entry><entry>132</entry><entry>SSDSESESSSEDSDSSSSSSDSESESSSEGSDSSSSSSSSESESSSEDNDSSSSSSDSES</entry><entry>191</entry></row><row><entry /></row><row><entry>Query:</entry><entry>82</entry><entry>TEPSQPSPSEENKPDGRTKTE---IGNNKDISSGTKVLISEDSIKNFSKASSDQEEVDRD</entry><entry>138</entry></row><row><entry /><entry /><entry>   S+ S S  +  D  +++      ++   SS      SED+  + S + S+ E    D</entry></row><row><entry>Sbjct:</entry><entry>192</entry><entry>ESSSEDSDSSSSSSDSESESSSEGSDSSSSSSSSESESSSEDNDSSSSSSDSESESSSED</entry><entry>251</entry></row><row><entry /></row><row><entry>Query:</entry><entry>139</entry><entry>ESSSSKANDGK-KGHSKPKKELPKTGDSHSDT</entry><entry>169</entry></row><row><entry /><entry /><entry>  SSS ++D + +  SK       + DS  D+</entry></row><row><entry>Sbjct:</entry><entry>252</entry><entry>SDSSSSSSDSESESSSKDSDSSSNSSDSEDDS</entry><entry>283</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 1984.

A related GBS gene &lt;SEQ ID 8785&gt; and protein &lt;SEQ ID 8786&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00004" num="00004"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="357pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1   Crend: 5</entry><entry /></row><row><entry>McG: Discrim Score: 6.72</entry></row><row><entry>GvH: Signal Score (−7.5): −4.34</entry></row><row><entry>Possible site: 27</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="91pt" align="left" /><colspec colname="2" colwidth="133pt" align="left" /><colspec colname="3" colwidth="133pt" align="left" /><colspec colname="4" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>ALOM program count: 1</entry><entry>value: −0.48</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="91pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="56pt" align="left" /><colspec colname="5" colwidth="77pt" align="left" /><colspec colname="6" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −0.48</entry><entry>Transmembrane</entry><entry>169-185</entry><entry>(169-185)</entry><entry /></row><row><entry>PERIPHERAL</entry><entry>Likelihood =  0.16</entry><entry>7</entry><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="357pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 0.60</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.1192 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 2 (GBS4) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 9</figref> (lane 3; MW 43.1 kDa) and <figref idrefs="DRAWINGS">FIG. 63</figref> (lane 4; MW 50 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 12</figref> (lane 7; MW 30 kDa), <figref idrefs="DRAWINGS">FIG. 63</figref> (lane 3; MW 30 kDa) and in <figref idrefs="DRAWINGS">FIG. 178</figref> (lane 3; MW 30 kDa).

GBS4-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 190</figref> (lane 6) and <figref idrefs="DRAWINGS">FIG. 209</figref> (lane 8).

Purified GBS4-His is shown in <figref idrefs="DRAWINGS">FIGS. 89A</figref>, <b>191</b> (lane 10), <b>209</b> (lane 7) and <b>228</b> (lanes 9 &amp; 10).

The purified GBS4-His fusion product was used to immunise mice (lane 2 product; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 89B</figref>), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 2

A DNA sequence (GBSx1100) was identified in <i>S. agalactiae </i>&lt;SEQ ID 3&gt; which encodes the amino acid sequence &lt;SEQ ID 4&gt;. This protein is predicted to be aggregation promoting protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00005" num="00005"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 33</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database.

<tables id="TABLE-US-00006" num="00006"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA69725 GB:Y08498 aggregation promoting protein</entry><entry /></row><row><entry>[<i>Lactobacillus gasseri</i>]</entry></row><row><entry>Identities = 56/103 (54%), Positives = 69/103 (66%), Gaps = 5/103 (4%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="right" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="right" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>82</entry><entry>TASQAEAKSQPT-----IENSMNSSSNLSSSDSAAKEEIARRESNGSYTAQNGQYYGRYQ</entry><entry>136</entry><entry /></row><row><entry /><entry /><entry>T S A A+ Q T      + + + + N S S++AAK  +A RES G Y+A NGQY G+YQ</entry><entry /></row><row><entry>Subj:</entry><entry>195</entry><entry>TYSTASAQKQTTQVAQKTQTTTSYTLNASGSEAAAKAWMAGRESGGPYSAGNGQYIGKYQ</entry><entry>254</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>LSQSYLNGDLSPENQEKVADNYVVSRYGSWSAALSFWNSNGWY</entry><entry>179</entry></row><row><entry /><entry /><entry>LS SYL GD S  NQE+VADNYV SRYGSW+ A  FW +NGWY</entry><entry /></row><row><entry>Sbjct:</entry><entry>255</entry><entry>LSASYLGGDYSAANQERVADNYVKSRYGSWTGAQKFWQTNGWY</entry><entry>297</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8709&gt; and protein &lt;SEQ ID 8710&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00007" num="00007"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1   Crend: 9</entry><entry /></row><row><entry>McG: Discrim Score: 2.59</entry></row><row><entry>GvH: Signal Score (−7.5): −0.42</entry></row><row><entry>Possible site: 33</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="133pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>ALOM program count: 0</entry><entry>value: 6.79</entry><entry>threshold: 0.0</entry><entry /></row><row><entry>PERIPHERAL</entry><entry>Likelihood = 6.79</entry><entry>59</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −1.86</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00001" num="00001"><img id="EMI-C00001" he="81.62mm" wi="120.14mm" file="US07939087-20110510-C00001.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00001" attachment-type="cdx" file="US07939087-20110510-C00001.CDX" /><attachment idref="CHEM-US-00001" attachment-type="mol" file="US07939087-20110510-C00001.MOL" /></attachments></chemistry>

A related GBS gene &lt;SEQ ID 8711&gt; and protein &lt;SEQ ID 8712&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00008" num="00008"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 9</entry><entry /></row><row><entry>McG: Discrim Score: 2.59</entry></row><row><entry>GvH: Signal Score (−7.5): −0.42</entry></row><row><entry>     Possible site: 33</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry>ALOM program count: 0 value: 6.79 threshold: 0.0</entry></row><row><entry>   PERIPHERAL Likelihood = 6.79 59</entry></row><row><entry>modified ALOM score: −1.86</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00002" num="00002"><img id="EMI-C00002" he="103.12mm" wi="120.14mm" file="US07939087-20110510-C00002.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00002" attachment-type="cdx" file="US07939087-20110510-C00002.CDX" /><attachment idref="CHEM-US-00002" attachment-type="mol" file="US07939087-20110510-C00002.MOL" /></attachments></chemistry>

SEQ ID 8712 (GBS166) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 30</figref> (lane 2; MW 13.1 kDa).

The GBS166-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 200</figref>, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 315</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

SEQ ID 4 (GBS15) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 9</figref> (lane 5; MW 44.8 kDa), <figref idrefs="DRAWINGS">FIG. 63</figref> (lane 5; MW 44.8 kDa) and <figref idrefs="DRAWINGS">FIG. 66</figref> (lane 7; MW 45 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 10</figref> (lane 4; MW 22.3 kDa). It was also expressed as GBS15L, with SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 185</figref> (lane 1; MW 50 kDa).

Purified GBS15-GST is shown in <figref idrefs="DRAWINGS">FIG. 91A</figref>, <figref idrefs="DRAWINGS">FIG. 190</figref> (lane 9), <figref idrefs="DRAWINGS">FIG. 210</figref> (lane 4) and <figref idrefs="DRAWINGS">FIG. 245</figref> (lanes 4 &amp; 5).

The purified GBS15-GST fusion product was used to immunise mice (lane 1+2 products; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 91B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 91C</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 3

A DNA sequence (GBSx0091) was identified in <i>S. agalactiae </i>&lt;SEQ ID 303&gt; which encodes the amino acid sequence &lt;SEQ ID 304&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00009" num="00009"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.66</entry><entry>Transmembrane</entry><entry>22-38 (15-41)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4864(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00010" num="00010"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA72096 GB: Y11213 hypothetical protein [<i>Streptococcus thermophilus</i>]</entry><entry /></row><row><entry>Identities = 149/274 (54%), Positives = 208/274 (75%), Gaps = 9/274 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>23</entry><entry>FLVSLLLSFGIFSLIIPKSNP--KLTKKDFLTKKVIPLNYVALGDSLTEGVGDTTSQGGF</entry><entry>80</entry><entry /></row><row><entry /><entry /><entry>F +  LL  GI   IIP S+   K++ K    KK   + YVA+GDSLT+GVGD+++QGGF</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>FFLLFLLFVGILIFIIPSSHQSSKISDKIRSVKKE-KVTYVAIGDSLTQGVGDSSNQGGF</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>81</entry><entry>VPLLSESLHNRYSYQVTSVNYGVSGNTSQQILKRMTTDPQIEKDLEKADLLTLTVGGNDV</entry><entry>140</entry></row><row><entry /><entry /><entry>VP+LS++L + +++QVT  NYG++GNTS QILKRM     I++DL+KA L+TLTVGGNDV</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>VPVLSQALESDFNWQVTPRNYGIAGNTSNQILKRMQEKKDIKRDLKKAKLMTLTVGGNDV</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>141</entry><entry>LAVIRKELSHLSLNSFEKPAEAYKERLKEILAKARQDNPKLPIYVLGIYNPFYLNFPQLT</entry><entry>200</entry></row><row><entry /><entry /><entry>+ VI+  +++L++N+F K A  Y++RL++I+  AR++N  LPIY++GIYNPFYLNEP++T</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>IHVIKDNITNLNVNTFSKAAVDYQKRLRQIIELARKENKTLPIYIIGIYNPFYLNFPEMT</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>201</entry><entry>KMQTVIDNWNKATKEVVDASENVYFVPINDRLYKGINGKEGITES------SNSQASITN</entry><entry>254</entry></row><row><entry /><entry /><entry>+MQT++DNWN++T+EV    +NVYFVP+ND LYKGINGK G+T S      + S     N</entry></row><row><entry>Sbjct:</entry><entry>184</entry><entry>EMQTIVDNWNRSTEEVSKEYDNVYFVPVNDLLYKGINGKGGVTSSDETSQPTKSSQDSLN</entry><entry>243</entry></row><row><entry /></row><row><entry>Query:</entry><entry>255</entry><entry>DALFTGDHFHPNNIGYQIMSNAVMEKINETRKNW</entry><entry>288</entry></row><row><entry /><entry /><entry>DALF  DHFHPNN GYQIMS+A++++IN+T+K W</entry></row><row><entry>Sbjct:</entry><entry>244</entry><entry>DALFEEDHFNPNNTGYQIMSDAILKRINQTKKEW</entry><entry>277</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 305&gt; which encodes the amino acid sequence &lt;SEQ ID 306&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00011" num="00011"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have en uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.05</entry><entry>Transmembrane</entry><entry>18-34 (10-37)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5819(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related sequence was also identified in GAS &lt;SEQ ID 9123&gt; which encodes the amino acid sequence &lt;SEQ ID 9124&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00012" num="00012"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 33</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="56pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.05</entry><entry>Transmembrane</entry><entry>12-28</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5819(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00013" num="00013"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 178/282 (63%), Positives = 218/282 (77%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>LLLWFVMNKKKILTGLSFFLVSLLLSFGIFSLIIPKSNPKLTKKDFLTKKVIPLNYVALG</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>L LWFVMN + + +G+ FF++SL L+F + ++IIPKSN +L K DFL K+ + + YVA+G</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LRLWFVMNNRHLFSGIFFFVISLCLAFLLLNIIIPKSNSRLKKSDFLKKEQVAIQYVAIG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>DSLTEGVGDTTSQGGFVPLLSESLHNRYSYQVTSVNYGVSGNTSQQILKRMTTDPQIEKD</entry><entry>124</entry></row><row><entry /><entry /><entry>DSLTEGVGD T QGGFVPLL+  L   +   V   NYGVSG+TSQQIL RM    QI+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DSLTEGVGDLTHQGGFVPLLTNDLSEYFKANVNHQNYGVSGDTSQQILDRMIKQKQIQLS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LEKADLLTLTVGGNDVLAVIRKELSHLSLNSFEKPAEAYKERLKEILAKARQDNPKLPIY</entry><entry>184</entry></row><row><entry /><entry /><entry>L+KAD++TLTVGGNDV+AVIRK L+ L ++SF KPA  Y++RL++I+  AR+DN  LPI+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LKKADIMTLTVGGNDVMAVIRKNLADLQVSSFRKPARQYQKRLRQIIELARKDNKDLPIF</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>VLGIYNPFYLNFPQLTKMQTVIDNWNKATKEVVDASENVYFVPINDRLYKGINGKEGITE</entry><entry>244</entry></row><row><entry /><entry /><entry>+LGIYNPFYLNFP+LT MQ VID+WN  TKEVV   + VYFVPIND LYKGING+EGI</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>ILGIYNPFYLNFPELTDMQKVIDDWNTKTKEVVGEYDRVYFVPINDLLYKGINGQEGIVH</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>SSNSQASITNDALFTGDHFHPNNIGYQIMSNAVMEKINETRK</entry><entry>286</entry></row><row><entry /><entry /><entry>SS  Q +I NDALFTGDHFHPNN GYQIMSNAVMEKI +  K</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>SSGDQTTIVNDALFTGDHFHPNNTGYQIMSNAVMEKIKKHEK</entry><entry>282</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 5&gt; and protein &lt;SEQ ID 6&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00014" num="00014"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 4</entry><entry /></row><row><entry>SRCFLG: 0</entry></row><row><entry>McG: Length of UR: 24</entry></row><row><entry>     Peak Value of UR: 3.02</entry></row><row><entry>     Net Charge of CR: 3</entry></row><row><entry>McG: Discrim Score: 12.27</entry></row><row><entry>GvH: Signal Score (−7.5): −3.44</entry></row><row><entry>     Possible site: 22</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry>Amino Acid Composition: calculated from 1</entry></row><row><entry>ALOM program Count: 1 value: −9.66 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = 9.66</entry><entry>Transmembrane</entry><entry>12-28 (5-31)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 1.96</entry><entry>118</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.43</entry><entry /></row><row><entry>icm1 HYPID: 7 CFP: 0.486</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.4864(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00003" num="00003"><img id="EMI-C00003" he="100.33mm" wi="118.87mm" file="US07939087-20110510-C00003.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00003" attachment-type="cdx" file="US07939087-20110510-C00003.CDX" /><attachment idref="CHEM-US-00003" attachment-type="mol" file="US07939087-20110510-C00003.MOL" /></attachments></chemistry>

SEQ ID 6 (GBS103) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 36</figref> (lane 4; MW 32 kDa).

The GBS103-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 107A</figref>; see also <figref idrefs="DRAWINGS">FIG. 201</figref>, lane 9) and used to immunise mice (lane 2+3 product; 18.5 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 107B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 107C</figref>) and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 4

A DNA sequence (GBSx1316) was identified in <i>S. agalactiae </i>&lt;SEQ ID 3837&gt; which encodes the amino acid sequence &lt;SEQ ID 3838&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00015" num="00015"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>1058-1074 (1056-1075)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2720(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 7&gt; and protein &lt;SEQ ID 8&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00016" num="00016"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: −13.26</entry></row><row><entry>GvH: Signal Score (−7.5): −5.76</entry></row><row><entry>     Possible site: 41</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 1 value: −4.30 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>489-505 (487-506)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 3.71</entry><entry>97</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 1.36</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.2720(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>LPXTG motif: 478-482</entry></row></tbody></tgroup></table></tables>

SEQ ID 8 (GBS195) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 24</figref> (lane 8). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 31</figref> (lane 5).

GBS195C was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 175</figref> (lane 6 &amp; 7; MW 81 kDa).

GBS195L was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 83</figref> (lane 2; MW 123 kDa).

GBS195LN was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 83</figref> (lane 3; MW 66 kDa).

GBS195-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 198</figref>, lane 5. GBS195-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 222</figref>, lane 4-5. GBS195N-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 222</figref>, lane 6-7.

The GBS195-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 87A</figref>) and used to immunise mice (lane 1 product; 13.6 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 87B</figref>), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 5

A DNA sequence (GBSx0002) was identified in <i>S. agalactiae </i>&lt;SEQ ID 4043&gt; which encodes the amino acid sequence &lt;SEQ ID 4044&gt;. This protein is predicted to be lipoprotein MtsA. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00017" num="00017"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3361(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9403&gt; which encodes amino acid sequence &lt;SEQ ID 9404&gt; was also identified.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 3177&gt; which encodes the amino acid sequence &lt;SEQ ID 3178&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00018" num="00018"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2412 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00019" num="00019"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 146/168 (86%), Positives = 161/168 (94%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNLENGIIYSKNIAKQLIAKDPKNKATYEKNRDAYVAKLEKLDKEAKSKFNAIPANKKLI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+NLENGIIYSKNIAKQLIAKDPKNK TYEKN  AYVAKLEKLDKEAKSKF+AI  NKKLI</entry></row><row><entry>Sbjct:</entry><entry>107</entry><entry>LNLENGIIYSKNIAKQLIAKDPKNKETYEKNLKAYVAKLEKLDKEAKSKFDAIAENKKLI</entry><entry>166</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQITSLVKKLKQVRPSALFVESSVDKRP</entry><entry>120</entry></row><row><entry /><entry /><entry>VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQI+SL++KLK ++PSALFVESSVD+RP</entry></row><row><entry>Sbjct:</entry><entry>167</entry><entry>VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQISSLIEKLKVIKPSALFVESSVDRRP</entry><entry>226</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>MKSVSRESGIPIYAEIFTDSIAKKGQKGDSYYAMMKWNLDKIAEGLAK</entry><entry>168</entry></row><row><entry /><entry /><entry>M++VS++SGIPIY+EIFTDSIAKKG+ GDSYYAMMKWNLDKI+EGLAK</entry></row><row><entry>Sbjct:</entry><entry>227</entry><entry>METVSKDSGIPIYSEIFTDSIAKKGKPGDSYYAMMKWNLDKISEGLAK</entry><entry>274</entry></row></tbody></tgroup></table></tables>

SEQ ID 9404 (GBS679) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 164</figref> (lane 7-9; MW 36 kDa) and in <figref idrefs="DRAWINGS">FIG. 188</figref> (lane 8; MW 36 kDa). Purified protein is shown in <figref idrefs="DRAWINGS">FIG. 242</figref>, lanes 9 &amp; 10.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 6

A DNA sequence (GBSx0003) was identified in <i>S. agalactiae </i>&lt;SEQ ID 8485&gt; which encodes the amino acid sequence &lt;SEQ ID 8486&gt;. This protein is predicted to be ATP-binding protein MtsB. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00020" num="00020"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2097 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 8765&gt; which encodes the amino acid sequence &lt;SEQ ID 8766&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00021" num="00021"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1929 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00022" num="00022"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 143/238 (60%), Positives = 186/238 (78%), Gaps = 2/238 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MIISKHLSVSYDNNL-VLEDINLRLEGSGIIGILGPNGAGKSTLMKALLGLVDSTGESGI</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>MI + +L V+YD N   LE IN+ +EG  I+GI+GPNGAGKST MKA+L L+D  G   +</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>MITTNNLCVTYDGNSNALEAINVTIEGPSIVGIIGPNGAGKSTFMKAILNLIDYQGHVTV</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>GG-DLLPLMGRVAYVEQKTNIDYQFPITVGECVSLGLYKERGLFKRLSKTDWEKVSRVID</entry><entry>118</entry></row><row><entry /><entry /><entry> G D   L   VAYVEQ++ IDY FPITV ECV+LG Y + GLF+R+ K  +E+V +V+</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>DGKDGRKLGHTVAYVEQRSMIDYNFPITVKECVALGTYSKLGLFRRVGKKQFEQVDKVLK</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>QVGLRGFENRPINALSGGQFQRMLMARCLVQEADYIFLDEPFVGIDSISEQIIVNLLKKL</entry><entry>178</entry></row><row><entry /><entry /><entry>QVGL  F +RPI +LSGGQFQRML+ARCL+QE+DYIFLDEPFVGIDS+SE+IIV+LLK+L</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>QVGLEDFGHRPIKSLSGGQFQRMLVARCLIQESDYIFLDEPFVGIDSVSEKIIVDLLKEL</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>179</entry><entry>SKAGKLILVVHHDLSKVDHYFDQVIILNRHLIACGPIDQAFTRENLSAAYGDAILLGQ</entry><entry>236</entry></row><row><entry /><entry /><entry>  AGK IL+VHHDLSKV+HYFD+++ILN+HL+A G + + FT + LS AYG+ ++LG+</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>KMAGKTILIVHHDLSKVEHYFDKLMILNKHLVAYGNVCEVFTVDTLSKAYGNHLILGK</entry><entry>247</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 7

A DNA sequence (GBSx0004) was identified in <i>S. agalactiae </i>&lt;SEQ ID 9&gt; which encodes the amino acid sequence &lt;SEQ ID 10&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00023" num="00023"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 8

A DNA sequence (GBSx0005) was identified in <i>S. agalactiae </i>&lt;SEQ ID 11&gt; which encodes the amino acid sequence &lt;SEQ ID 12&gt;. This protein is predicted to be integral membrane protein MtsC (znuB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00024" num="00024"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 6</entry><entry /></row><row><entry>McG: Discrim Score: 3.77</entry></row><row><entry>GvH: Signal Score (−7.5): −0.47</entry></row><row><entry>     Possible site: 45</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.83</entry><entry>Transmembrane</entry><entry>138-154 (134-162)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.96</entry><entry>Transmembrane</entry><entry>  60-76 (50-86)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.95</entry><entry>Transmembrane</entry><entry> 95-111 (93-118)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry>180-196 (174-216)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.35</entry><entry>Transmembrane</entry><entry>198-214 (197-216)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>250-266 (246-268)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.93</entry><entry>Transmembrane</entry><entry>222-238 (221-241)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 5.94</entry><entry>116</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.67</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.5331(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 13&gt; which encodes the amino acid sequence &lt;SEQ ID 14&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00025" num="00025"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.25</entry><entry>Transmembrane</entry><entry>138-154 (134-163)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.08</entry><entry>Transmembrane</entry><entry>  66-82 (50-86)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.79</entry><entry>Transmembrane</entry><entry> 95-111 (93-118)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.63</entry><entry>Transmembrane</entry><entry>180-196 (176-216)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.73</entry><entry>Transmembrane</entry><entry>221-237 (218-241)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.35</entry><entry>Transmembrane</entry><entry>250-266 (246-268)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.35</entry><entry>Transmembrane</entry><entry>198-214 (197-216)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.81</entry><entry>Transmembrane</entry><entry>  48-64 (47-64)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5501(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00026" num="00026"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 224/275 (81%), Positives = 255/275 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MFTKFFEGLLTYHFLQNAFITAIVIGIVAGAVGCFIILRSMSLMGDAISHAVLPGVAISF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  KFFEGL++YHFLQNA ITA+VIGIV+GAVGCFIILRSMSLMGDAISHAVLPGVA+SF</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSMKFFEGLMSYHFLQNALITAVVIGIVSGAVGCFIILRSMSLMGDAISHAVLPGVALSF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>ILGINFFIGAIVFGLLSSIIITYIKENSVIKGDTAIGITFSSFLALGIILIGLANSTTDL</entry><entry>120</entry></row><row><entry /><entry /><entry>ILG+NFFIGAI+FGLL+S+IITYIKENSVIKGDTAIGITFSSFLALG+ILIG+ANS+TDL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ILGVNFFIGAIIFGLLASVIITYIKENSVIKGDTAIGITFSSFLALGVILIGVANSSTDL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>FHILFGNILAVQDSDKYMTIIVGLIVLTLITIFFKELLLTSFDPVLAKSMGMRVSFYHYL</entry><entry>180</entry></row><row><entry /><entry /><entry>FHILFGNILAVQDSDK++TI V + VL +I++FFKELLLTSFDP+LAKSMG++V+ YHYL</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>FHILFGNILAVQDSDKWITIGVSIFVLVVISLFFKELLLTSFDPILAKSMGVKVNAYHYL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LMILLTLVAVTAMQSVGTILIVALLITPAATAYLYVKSLRTMLFLSSALGAVASVLGLYI</entry><entry>240</entry></row><row><entry /><entry /><entry>LM+LLTLVAVTAMQSVGTILIVALLITPAATAYLY  SL+ ML +SS LGA+ASVLGLY+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LMVLLTLVAVTAMQSVGTILIVALLITPAATAYLYANSLKVMLVMSSLLGALASVLGLYL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GYTFNIAAGSSIVLTSTFMFLLAFLFSPKQSLFKK</entry><entry>275</entry></row><row><entry /><entry /><entry>GYTFN+AAGSSIVLTS  MFL++F  SPKQ   K+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GYTFNVAAGSSIVLTSAMMFLISFFVSPKQGYLKR</entry><entry>275</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 9

A DNA sequence (GBSx0006) was identified in <i>S. agalactiae </i>&lt;SEQ ID 15&gt; which encodes the amino acid sequence &lt;SEQ ID 16&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00027" num="00027"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1280(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 10

A DNA sequence (GBSx0007) was identified in <i>S. agalactiae </i>&lt;SEQ ID 17&gt; which encodes the amino acid sequence &lt;SEQ ID 18&gt;. This protein is predicted to be peptidyl-prolyl cis-trans isomerase 10 (rotamase). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00028" num="00028"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop Possible site: 19 Crend: 2</entry><entry /></row><row><entry>McG: Discrim Score: 5.27</entry></row><row><entry>GvH: Signal Score (−7.5): −4.14</entry></row><row><entry>Possible site: 19</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 0</entry><entry>value: 9.34</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 9.34</entry><entry>89</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −2.37</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00029" num="00029"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA19257 GB: AL023704 putative Cyclophilin-type peptidyl-prolyl</entry><entry /></row><row><entry>cis-trans isomerase protein [<i>Schizosaccharomyces pombe</i>]</entry></row><row><entry>Identities = 88/224 (39%), Positives = 123/224 (54%), Gaps = 46/224 (20%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>50</entry><entry>NKKTKQALKADKKAFPQLDKAVAKNEAQ-----------VLIKTSKGDINIKLFPKYAPL</entry><entry>98</entry><entry /></row><row><entry /><entry /><entry>N  TK  L +D+  + +    V  NE +            +I T++GDI+IKL+P+ AP</entry></row><row><entry>Sbjct:</entry><entry>419</entry><entry>NMSTKFTL-SDRDVYNEQVLPVTNNEGRQENGNILLGKAAIIHTTQGDISIKLYPEEAPK</entry><entry>477</entry></row><row><entry /></row><row><entry>Query:</entry><entry>99</entry><entry>AVENFLTHAKEGYYNGLSFHRVIKDFMIQSGDPNGDGTGGKSIWNSKDKKKDSGNGFVNE</entry><entry>158</entry></row><row><entry /><entry /><entry>AV+NF THA+ GYY+   FHR+IK+FMIQ GDP GDGTGG+SIW     KKD    F +E</entry></row><row><entry>Sbjct:</entry><entry>478</entry><entry>AVQNFTTHAENGYYDNTIFHRIIKNFMIQGGDPLGDGTGGESIW-----KKD----FEDE</entry><entry>528</entry></row><row><entry /></row><row><entry>Query:</entry><entry>159</entry><entry>ISPYLYNIRG-SLAMANAGADTNGSQFFINQSQQDHSKQLSDKKVPKVIIKAYSEGGNPS</entry><entry>217</entry></row><row><entry /><entry /><entry>ISP L + R  +++MAN+G +TNGSQFFI                             P</entry></row><row><entry>Sbjct:</entry><entry>529</entry><entry>ISPNLKHDRPFTVSMANSGPNTNGSQFFITTDL------------------------TPW</entry><entry>564</entry></row><row><entry /></row><row><entry>Query:</entry><entry>218</entry><entry>LDGGYTVFGQVISGMETVDKIASVEVTKSDQPKEKITITSIKVI</entry><entry>261</entry></row><row><entry /><entry /><entry>LDG +T+F +  +G++ V +I   E  K D+P E   I +I ++</entry></row><row><entry>Sbjct:</entry><entry>565</entry><entry>LDGKHTIFARAYAGLDVVHRIEQGETDKYDRPLEPTKIINISIV</entry><entry>608</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 19&gt; which encodes the amino acid sequence &lt;SEQ ID 20&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00030" num="00030"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00031" num="00031"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB88542 GB: AL353818 putative protein [<i>Arabidopsis thaliana</i>]</entry><entry /></row><row><entry>Identities = 83/186 (44%), Positives = 104/186 (55%), Gaps = 34/186 (18%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>78</entry><entry>VVMRTSQGDITLKLFPKYAPLAVENFLTHAKKGYYDNLTFHRVINDFMIQSGDPKGDGTG</entry><entry>137</entry><entry /></row><row><entry /><entry /><entry>V+M T+ GDI +KL+P+  P  VENF TH + GYYDN  FHRVI  FMIQ+GDP GDGTG</entry></row><row><entry>Sbjct:</entry><entry>476</entry><entry>VIMHTTLGDIHMKLYPEECPKTVENFTTHCRNGYYDNHLFHRVIRGFMIQTGDPLGDGTG</entry><entry>535</entry></row><row><entry /></row><row><entry>Query:</entry><entry>138</entry><entry>GESIWKGKDPKKDAGNGFVNEISPFLYHIRG-ALAMANAGANTNGSQFYINQNKKNQSKG</entry><entry>196</entry></row><row><entry /><entry /><entry>G+SIW         G  F +E    L H R   L+MANAG NTNGSQF+I</entry></row><row><entry>Sbjct:</entry><entry>536</entry><entry>GQSIW---------GREFEDEFHKSLRHDRPFTLSMANAGPNTNGSQFFITT--------</entry><entry>578</entry></row><row><entry /></row><row><entry>Query:</entry><entry>197</entry><entry>LSSTNYPKPIISAYEHGGNPSLDGGYTVFGQVIDGMDVVDKIAATSINQNDKPEQDITIT</entry><entry>256</entry></row><row><entry /><entry /><entry>                   P LD  +TVFG+V+ GMDVV  I     ++ND+P QD+ I</entry></row><row><entry>Sbjct:</entry><entry>579</entry><entry>----------------VATPWLDNKHTVFGRVVKGMDVVQGIEKVKTDKNDRPYQDVKIL</entry><entry>622</entry></row><row><entry /></row><row><entry>Query:</entry><entry>257</entry><entry>SIDIVK</entry><entry>262</entry></row><row><entry /><entry /><entry>++ + K</entry></row><row><entry>Sbjct:</entry><entry>623</entry><entry>NVTVPK</entry><entry>628</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00032" num="00032"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 172/267 (64%), Positives 221/267 (82%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKKIIYLGLACVSILTLSGCESIERSLKGDRYVDQKLAENSSKEATEQLNKKTKQALKAD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKK++ L L  +S+L LS CES++R++KGD+Y+D+K A+  S+ A++   +  ++ALKAD</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKKLLSLSLVAISLLNLSACESVDRAIKGDKYIDEKTAKEESEAASKAYEESIQKALKAD</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KKAFPQLDKAVAKNEAQVLIKTSKGDINIKLFPKYAPLAVENFLTHAKEGYYNGLSFHRV</entry><entry>120</entry></row><row><entry /><entry /><entry>   FPQL K V K EA+V+++TS+GDI +KLFPKYAPLAVENFLTHAK+GYY+ L+FHRV</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ASQFPQLTKEVGKEEAKVVMRTSQGDITLKLFPKYAPLAVENFLTHAKKGYYDNLTFHRV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IKDFMIQSGDPNGDGTGGKSIWNSKDKKKDSGNGFVNEISPYLYNIRGSLAMANAGADTN</entry><entry>180</entry></row><row><entry /><entry /><entry>I DFMIQSGDP GDGTGG+SIW  KD KKD+GNGFVNEISP+LY+IRG+LAMANAGA+TN</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>INDFMIQSGDPKGDGTGGESIWKGKDPKKDAGNGFVNEISPFLYHIRGALAMANAGANTN</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>GSQFFINQSQQDHSKQLSDKKVPKVIIKAYSEGGNPSLDGGYTVFGQVISGMETVDKIAS</entry><entry>240</entry></row><row><entry /><entry /><entry>GSQF+INQ++++ SK LS    PK II AY  GGNPSLDGGYTVFGQVI GM+ VDKIA+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>GSQFYINQNKKNQSKGLSSTNYPKPIISAYEHGGNPSLDGGYTVFGQVIDGMDVVDKIAA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VEVTKSDQPKEKITITSIKVIKDYKFK</entry><entry>267</entry></row><row><entry /><entry /><entry>  + ++D+P++ ITITSI ++KDY+FK</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>TSINQNDKPEQDITITSIDIVKDYRFK</entry><entry>267</entry></row></tbody></tgroup></table></tables>

SEQ ID 18 (GBS205) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 51</figref> (lane 13; MW 31 kDa).

GBS205-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 206</figref>, lane 8.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 11

A DNA sequence (GBSx0008) was identified in <i>S. agalactiae </i>&lt;SEQ ID 21&gt; which encodes the amino acid sequence &lt;SEQ ID 22&gt;. This protein is predicted to be sporulation protein SpoIIIE (ftsK). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00033" num="00033"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop Possible site: −1  Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: −22.83</entry></row><row><entry>GvH: Signal Score (−7.5): −7.13</entry></row><row><entry>   Possible site: 39</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program  count: 5  value: −9.24  threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="7"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="-7pt" align="left" /><colspec colname="5" colwidth="140pt" align="left" /><colspec colname="6" colwidth="70pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.24</entry><entry>Transmembrane</entry><entry> 36-52</entry><entry> (27-60)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.18</entry><entry>Transmembrane</entry><entry>162-178</entry><entry>(154-188)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.04</entry><entry>Transmembrane</entry><entry>597-613</entry><entry>(595-615)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry> 63-79</entry><entry> (58-83)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.60</entry><entry>Transmembrane</entry><entry> 90-106</entry><entry> (88-108)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = −1.32</entry><entry>136</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.35</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.4694 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10035&gt; which encodes amino acid sequence &lt;SEQ ID 10036&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<chemistry id="CHEM-US-00004" num="00004"><img id="EMI-C00004" he="215.14mm" wi="112.95mm" file="US07939087-20110510-C00004.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00004" attachment-type="cdx" file="US07939087-20110510-C00004.CDX" /><attachment idref="CHEM-US-00004" attachment-type="mol" file="US07939087-20110510-C00004.MOL" /></attachments></chemistry><chemistry id="CHEM-US-00005" num="00005"><img id="EMI-C00005" he="208.11mm" wi="118.62mm" file="US07939087-20110510-C00005.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00005" attachment-type="cdx" file="US07939087-20110510-C00005.CDX" /><attachment idref="CHEM-US-00005" attachment-type="mol" file="US07939087-20110510-C00005.MOL" /></attachments></chemistry>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 23&gt; which encodes the amino acid sequence &lt;SEQ ID 24&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00034" num="00034"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="42pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="63pt" align="left" /><colspec colname="4" colwidth="42pt" align="left" /><colspec colname="5" colwidth="42pt" align="left" /><colspec colname="6" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −9.45</entry><entry>Transmembrane</entry><entry> 31-47</entry><entry> (25-55)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −7.17</entry><entry>Transmembrane</entry><entry>160-176</entry><entry>(153-183)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry> 93-109</entry><entry> (86-111)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.04</entry><entry>Transmembrane</entry><entry>586-602</entry><entry>(584-604)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.22</entry><entry>Transmembrane</entry><entry> 64-80</entry><entry> (64-80)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.4779 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00035" num="00035"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="147pt" align="left" /><colspec colname="2" colwidth="14pt" align="left" /><colspec colname="3" colwidth="154pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>!GB:Z99112 DNA translocase [<i>Bacillus subtilis</i>]</entry><entry>601</entry><entry>e-170</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 354/816 (43%), Positives = 499/816 (60%),</entry><entry /></row><row><entry>Gaps = 69/816 (8%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="right" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="right" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>APKKRLTKAEVEKQRAIKRMILSVLMALLLIFAMLRLGVFGVTTYNMIRFLVGSLAYPFM</entry><entry>70</entry><entry /></row><row><entry /><entry /><entry>A KKR ++ +  KQ  IK  +  +L   + I A+L+LGV G T   + RF  G      +</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>AKKKRKSRKKQAKQLNIKYELNGLLCIAISIIAILQLGVVGQTFIYLFRFFAGEWFILCL</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>71</entry><entry>FAWLIYLFCFKWLRQKDGMI----AGVVIAFLGLLVEWHAFLFA----MPRMLDQDIFLG</entry><entry>122</entry></row><row><entry /><entry /><entry>   L+      W ++   ++    AG+      +L+  H  LF        +    +</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>LGLLVLGVSLFWKKKTPSLLTRRKAGLYCIIASILLLSHVQLFKNLTHKGSIESASVVRN</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>TARLITRDLLALRVTEFVGGGMLGALLYKPIAFLFSNIGSYFIGFLFILLGLFLMTPWDI</entry><entry>182</entry></row><row><entry /><entry /><entry>T  L   D+     +  +GGGM+GALL+    FLF++ GS  +  + IL+G+ L+T   +</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>TWELFLMDMNGSSASPDLGGGMIGALLFAASHFLFASTGSQIMAIVMILIGMILVTGRSL</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>YD--------VSHFVKEA----VDKLAVAYQENKEKRFIKREEHRLQAEKEALEKQAQEE</entry><entry>230</entry></row><row><entry /><entry /><entry> +        +  F+KE     +D +  +++ N +    K+ +   + +K A +KQ  E</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>QETLKKWMSPIGRFIKEQWLAFIDDMK-SFKSNMQSS--KKTKAPSKKQKPARKKQQMEP</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>231</entry><entry>EKRLAELTVDPETGEIVEDSQSQVSYDLAEDMT-KEPEILAYDSHLKDDETSLFDQ----</entry><entry>285</entry></row><row><entry /><entry /><entry>E          E G+          Y+    +   EP I ++    +++E+ + ++</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>EP-------PDEEGD----------YETVSPLIHSEPIISSFSDRNEEEESPVIEKRAEP</entry><entry>281</entry></row><row><entry /></row><row><entry>Query:</entry><entry>286</entry><entry>--EDLAYAHEEIGAYDSLSALASSEDEMDMDEPVEVDFTPKTHLLYKLPTIDLFAPDKPK</entry><entry>343</entry></row><row><entry /><entry /><entry>  +L     E G  +++SA   +  E++  +             Y++P++DL A  K</entry></row><row><entry>Sbjct:</entry><entry>282</entry><entry>VSKPLQDIQPETGDQETVSAPPMTFTELENKD-------------YEMPSLDLLADPKHT</entry><entry>328</entry></row><row><entry /></row><row><entry>Query:</entry><entry>344</entry><entry>NQSKEKNLVRKNIKVLEDTFQSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLADD</entry><entry>403</entry></row><row><entry /><entry /><entry> Q  +K  + +N + LE TFQSFG+  KV +  +GP+VTKYE+ P VGV+V++I NL+DD</entry></row><row><entry>Sbjct:</entry><entry>329</entry><entry>GQQADKKNIYENARKLERTFQSFGVKAKVTQVHLGPAVTKYEVYPDVGVKVSKIVNLSDD</entry><entry>388</entry></row><row><entry /></row><row><entry>Query:</entry><entry>404</entry><entry>LALALAAKDVRIEAPIPGKSLIGIEVPNSEIATVSFRELWEQS-DANPENLLEVPLGKAV</entry><entry>462</entry></row><row><entry /><entry /><entry>LALALAAKD+RIEAPIPGKS IGIEVPN+E+A VS +E+ E   +  P+  + + LG+ +</entry></row><row><entry>Sbjct:</entry><entry>389</entry><entry>LALALAAKDIRIEAPIPGKSAIGIEVPNAEVAMVSLKEVLESKLNDRPDANVLIGLGRNI</entry><entry>448</entry></row><row><entry /></row><row><entry>Query:</entry><entry>463</entry><entry>NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY</entry><entry>522</entry></row><row><entry /><entry /><entry>+G A    L +MPHLLVAG+TGSGKSV VNGII+SILM+A+P +VK MMIDPKMVEL+VY</entry></row><row><entry>Sbjct:</entry><entry>449</entry><entry>SGEAVLAELNKMPHLLVAGATGSGKSVCVNGIITSILMRAKPHEVKMMMIDPKMVELNVY</entry><entry>508</entry></row><row><entry /></row><row><entry>Query:</entry><entry>523</entry><entry>NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK</entry><entry>582</entry></row><row><entry /><entry /><entry>N IPHLL PVVT+P+KAS+AL+KVV+EME RYELFS  G RNI GYN  ++  N     K</entry></row><row><entry>Sbjct:</entry><entry>509</entry><entry>NGIPHLLAPVVTDPKKASQALKKVVNEMERRYELFSHTGTRNIEGYNDYIKRANNEEGAK</entry><entry>568</entry></row><row><entry /></row><row><entry>Query:</entry><entry>583</entry><entry>QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK</entry><entry>642</entry></row><row><entry /><entry /><entry>Q  LP IVVIVDELADLMMVAS +VED+I RL Q ARAAGIH+I+ATQRPSVDVI+G+IK</entry></row><row><entry>Sbjct:</entry><entry>569</entry><entry>QPELPYIVVIVDELADLMMVASSDVEDSITRLSQMARAAGIHLIIATQRPSVDVITGVIK</entry><entry>628</entry></row><row><entry /></row><row><entry>Query:</entry><entry>643</entry><entry>ANVPSRMAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER</entry><entry>702</entry></row><row><entry /><entry /><entry>AN+PSR+AF+VSS TDSRTILD  GAEKLLGRGDMLF P+  N PVR+QG+F+SDD+VE+</entry></row><row><entry>Sbjct:</entry><entry>629</entry><entry>ANIPSRIAFSVSSQTDSRTILDMGGAEKLLGRGDMLFLPVGANKPVRVQGAFLSDDEVEK</entry><entry>688</entry></row><row><entry /></row><row><entry>Query:</entry><entry>703</entry><entry>IVNFIKDQTEADYDDAFDPGEVSDNDPGFSGNGGAAEGDPLFEEAKALVLETQKASASMI</entry><entry>762</entry></row><row><entry /><entry /><entry>+V+ +  Q +A Y +   P E ++     +        D L++EA  L++  Q AS SM+</entry></row><row><entry>Sbjct:</entry><entry>689</entry><entry>VVDHVITQQKAQYQEEMIPEETTETHSEVT--------DELYDEAVELIVGMQTASVSML</entry><entry>740</entry></row><row><entry /></row><row><entry>Query:</entry><entry>763</entry><entry>QRRLSVGFNRATRLMDELEEAGVIGPAEGTKPRKVL</entry><entry>798</entry></row><row><entry /><entry /><entry>QRR  +G+ RA RL+D +EE GV+GP EG+KPR+VL</entry></row><row><entry>Sbjct:</entry><entry>741</entry><entry>QRRFRIGYTRAARLIDAMEERGVVGPYEGSKPREVL</entry><entry>776</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00036" num="00036"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 620/818 (75%), Positives = 701/818 (84%), Gaps = 25/818 (3%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVFMANKKKTKGKKTRRPTKAEIERQRAIQRMITALVLTIILFFGIIRLGIFGITVYNVI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MV    +KK+  KK  R TKAE+E+QRAI+RMI ++++ ++L F ++RLG+FG+T YN+I</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MVKRNQRKKSAPKK--RLTKAEVEKQRAIKRMILSVLMALLLIFAMLRLGVFGVTTYNMI</entry><entry>58</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>RFMVGSLAYLFIAATLIYLYFFKWLRKKDSLVAGFLIASLGLLIEWHAYLFSMPILKDKE</entry><entry>120</entry></row><row><entry /><entry /><entry>RF+VGSLAY F+ A LIYL+ FKWLR+KD ++AG +IA LGLL+EWHA+LF+MP + D++</entry></row><row><entry>Sbjct:</entry><entry>59</entry><entry>RFLVGSLAYPFMFAWLIYLFCFKWLRQKDGMIAGVVIAFLGLLVEWHAFLFAMPRMLDQD</entry><entry>118</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>ILRSTARLIVSDLMQFKITVFAGGGMLGALIYKPIAFLFSNIGAYMIGVLFIILGLFLMS</entry><entry>180</entry></row><row><entry /><entry /><entry>I   TARLI  DL+  ++T F GGGMLGAL+YKPIAFLFSNIG+Y IG LFI+LGLFLM+</entry></row><row><entry>Sbjct:</entry><entry>119</entry><entry>IFLGTARLITRDLLALRVTEFVGGGMLGALLYKPIAFLFSNIGSYFIGFLFILLGLFLMT</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SLEVYDIVEFIRAFKNKVAEKHEQNKKERFAKREMKKAIAEQERIERQKAEEEAYLASVN</entry><entry>240</entry></row><row><entry /><entry /><entry>  ++YD+  F++   +K+A  +++NK++RF KRE  +  AE+E +E+Q  EEE  LA +</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>PWDIYDVSHFVKEAVDKLAVAYQENKEKRFIKREEHRLQAEKEALEKQAQEEEKRLAELT</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VDPETGEILEDQAEDNLDDALPPEVSETSTPVFEPEILAYETSPQNDPLPV---EPTIYL</entry><entry>297</entry></row><row><entry /><entry /><entry>VDPETGEI+ED         +  +++E  T   EPEILAY++  ++D   +   E   Y</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>VDPETGEIVEDSQSQ-----VSYDLAEDMTK--EPEILAYDSHLKDDETSLFDQEDLAYA</entry><entry>291</entry></row><row><entry /></row><row><entry>Query:</entry><entry>298</entry><entry>ED----YDSPIPNMRENDEEMVYDLDDDVDDSDIENVDFTPKTTLVYKLPTIDLFAPDKP</entry><entry>353</entry></row><row><entry /><entry /><entry> +    YDS +  +  +++EM  D+D+ V+      VDFTPKT L+YKLPTIDLFAPDKP</entry></row><row><entry>Sbjct:</entry><entry>292</entry><entry>HEEIGAYDS-LSALASSEDEM--DMDEPVE------VDFTPKTHLLYKLPTIDLFAPDKP</entry><entry>342</entry></row><row><entry /></row><row><entry>Query:</entry><entry>354</entry><entry>KNQSKEKDLVRKNIRVLEETFRSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLSD</entry><entry>413</entry></row><row><entry /><entry /><entry>KNQSKEK+LVRKNI+VLE+TF+SFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNL+D</entry></row><row><entry>Sbjct:</entry><entry>343</entry><entry>KNQSKEKNLVRKNIKVLEDTFQSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLAD</entry><entry>402</entry></row><row><entry /></row><row><entry>Query:</entry><entry>414</entry><entry>DLALALAAKDVRIETPIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV</entry><entry>473</entry></row><row><entry /><entry /><entry>DLALALAAKDVRIE PIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV</entry></row><row><entry>Sbjct:</entry><entry>403</entry><entry>DLALALAAKDVRIEAPIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV</entry><entry>462</entry></row><row><entry /></row><row><entry>Query:</entry><entry>474</entry><entry>NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY</entry><entry>533</entry></row><row><entry /><entry /><entry>NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY</entry></row><row><entry>Sbjct:</entry><entry>463</entry><entry>NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY</entry><entry>522</entry></row><row><entry /></row><row><entry>Query:</entry><entry>534</entry><entry>NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK</entry><entry>593</entry></row><row><entry /><entry /><entry>NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK</entry></row><row><entry>Sbjct:</entry><entry>523</entry><entry>NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK</entry><entry>582</entry></row><row><entry /></row><row><entry>Query:</entry><entry>594</entry><entry>QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK</entry><entry>653</entry></row><row><entry /><entry /><entry>QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK</entry></row><row><entry>Sbjct:</entry><entry>583</entry><entry>QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK</entry><entry>642</entry></row><row><entry /></row><row><entry>Query:</entry><entry>654</entry><entry>ANVPSRIAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER</entry><entry>713</entry></row><row><entry /><entry /><entry>ANVPSR+AFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER</entry></row><row><entry>Sbjct:</entry><entry>643</entry><entry>ANVPSRMAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER</entry><entry>702</entry></row><row><entry /></row><row><entry>Query:</entry><entry>714</entry><entry>IVGFIKDQAEADYDDAFDPGEVSETDNGSGGGGGVPESDPLFEEAKGLVLETQKASASMI</entry><entry>773</entry></row><row><entry /><entry /><entry>IV FIKDQ EADYDDAFDPGEVS+ D G  G GG  E DPLFEEAK LVLETQKASASMI</entry></row><row><entry>Sbjct:</entry><entry>703</entry><entry>IVNFIKDQTEADYDDAFDPGEVSDNDPGFSGNGGAAEGDPLFEEAKALVLETQKASASMI</entry><entry>762</entry></row><row><entry /></row><row><entry>Query:</entry><entry>774</entry><entry>QRRLSVGFNRATRLMEELEAAGVIGPAEGTKPRKVLMT</entry><entry>811</entry></row><row><entry /><entry /><entry>QRRLSVGFNRATRLM+ELE AGVIGPAEGTKPRKVL T</entry></row><row><entry>Sbjct:</entry><entry>763</entry><entry>QRRLSVGFNRATRLMDELEEAGVIGPAEGTKPRKVLQT</entry><entry>800</entry></row></tbody></tgroup></table></tables>

SEQ ID 22 (GBS272d) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 147</figref> (lane 9; MW 55 kDa+lane 10; MW 70 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 147</figref> (lane 11 &amp; 13; MW 85 kDa+lane 12; MW 74 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 12

A DNA sequence (GBSx0009) was identified in <i>S. agalactiae </i>&lt;SEQ ID 25&gt; which encodes the amino acid sequence &lt;SEQ ID 26&gt;. This protein is predicted to be para-aminobenzoate synthetase (pabB) (pabB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00037" num="00037"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4073 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00038" num="00038"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD07357 GB: AE000547 para-aminobenzoate synthetase (pabB)</entry><entry /></row><row><entry>[<i>Helicobacter pylori </i>26695]</entry></row><row><entry>Identities = 204/580 (35%), Positives = 325/580 (55%), Gaps = 50/580 (8%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>16</entry><entry>YRFKNPTKELIADTLEQVLEVIKEVDYYQSQNYYVVGYLSYEASAAF-DSHFKVSQQKLA</entry><entry>74</entry><entry /></row><row><entry /><entry /><entry>++++   K+L A  L ++   +  +   +   Y+V GYL YEA  AF D +F+     L</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>FKYQKSVKKLTATNLNELKNALDFISQNRGNGYFV-GYLLYEARLAFLDENFQSQTPFLY</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>75</entry><entry>GEHLAY---FTVHKDCENEAFPLSYENVRLADNWTANVSEQEYQEAIANIKGQIRQGNTY</entry><entry>131</entry></row><row><entry /><entry /><entry> E       +++    E+  +P  +          +++ ++ Y +    +K +++ G+TY</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>FEQFLERKKYSLEPLKEHAFYPKIH----------SSLDQKTYFKQFKAVKERLKNGDTY</entry><entry>114</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>QVNYTLELSQQLCSDPFSVYERLMVEQGAGYNAYIAYDDKRILSVSPELFFKKK--DEVL</entry><entry>189</entry></row><row><entry /><entry /><entry>QVN T++L     + P  V++ ++  Q   + A+I  +   +LS SPELFF+ +  D  +</entry></row><row><entry>Sbjct:</entry><entry>115</entry><entry>QVNLTMDLFLDTKAKPKRVFKEVVHNQNTPFKAFIENEFGSVLSFSPELFFELEFLDTAI</entry><entry>174</entry></row><row><entry /></row><row><entry>Query:</entry><entry>190</entry><entry>T--TRPMKGTSARKPTYQEDVAERDWLANDPKNRSENMMIVDLLRNDMGRICDVGTVKVK</entry><entry>247</entry></row><row><entry /><entry /><entry>   T+PMKGT AR      D   R +L ND KNRSEN+MIVDLLRND+ R+    +VKV</entry></row><row><entry>Sbjct:</entry><entry>175</entry><entry>KIITKPMKGTIARSKNPLIDEKNRLFLQNDDKNRSENVMIVDLLRNDLSRLALKNSVKVN</entry><entry>234</entry></row><row><entry /></row><row><entry>Query:</entry><entry>248</entry><entry>KLCQVEQYATVWQMTSTIEGVLSPEVTLMSIFQALYPCGSITGAPKISTMAIINELEKRP</entry><entry>307</entry></row><row><entry /><entry /><entry>+L ++    +V+QM S IE  L  + +L  IF+AL+PCGS+TG PKI TM II  LEKRP</entry></row><row><entry>Sbjct:</entry><entry>235</entry><entry>QLFEIISLPSVYQMISEIEAKLPLKTSLFEIFKALFPCGSVTGCPKIKTMQIIESLEKRP</entry><entry>294</entry></row><row><entry /></row><row><entry>Query:</entry><entry>308</entry><entry>RGIYCGTIGLCMPDGQAIFNVPIRTVQMKGQQ--AYYGVGGGITWESQTDSEYEETRQKS</entry><entry>365</entry></row><row><entry /><entry /><entry>RG+YCG IG+ + + +A+F+VPIRT++ +  +   + GVG G+T++S+   EYEE+  KS</entry></row><row><entry>Sbjct:</entry><entry>295</entry><entry>RGVYCGAIGM-VEEKKALFSVPIRTLEKRVHENFLHLGVGSGVTYKSKAPKEYEESFLKS</entry><entry>353</entry></row><row><entry /></row><row><entry>Query:</entry><entry>366</entry><entry>-AVLTRVNPKFQLITTGRV--TENKLLFSQQ--HVERLVESASYFAYSFDKSKFERELKK</entry><entry>420</entry></row><row><entry /><entry /><entry>  V+ ++  +F+++ T ++   + KL  + +  H ERL+ S  YF + +D++  + EL</entry></row><row><entry>Sbjct:</entry><entry>354</entry><entry>FFVMPKI--EFEIVETMKIIKKDQKLEINNKNAHKERLMNSTRYFNFKYDENLLDFEL--</entry><entry>409</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>YLHQLDEKDYRLKIMLDKTGKVTFEVKQLVNLSKKFLTAEVVVQDYPI-KLSPFTYFKTS</entry><entry>479</entry></row><row><entry /><entry /><entry>      +EK+  L+++L+K GK+  E K L  L     + E+ + + PI K + F Y KT+</entry></row><row><entry>Sbjct:</entry><entry>410</entry><entry>------EKEGVLRVLLNKKGKLIKEYKTLEPLK----SLEIRLSEAPIDKRNDFLYHKTT</entry><entry>459</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>YRPHIIEGQN--------EKIFVSPEGLLLETSIGNIVLEKNGRFLTPDLSEGGLNGIYR</entry><entry>531</entry></row><row><entry /><entry /><entry>Y P   + +         ++IF + +  L E +  N+VLE + R LTP  S G LNG</entry></row><row><entry>Sbjct:</entry><entry>460</entry><entry>YAPFYQKARALIKKGVMFDEIFYNQDLELTEGARSNLVLEIHNRLLTPYFSAGALNGTGV</entry><entry>519</entry></row><row><entry /></row><row><entry>Query:</entry><entry>532</entry><entry>RHLLKNQKVIEAPLTLKDLESADAIYACNAVRGLYPLNLK</entry><entry>571</entry></row><row><entry /><entry /><entry>  LLK   V  APL L+DL+ A  IY  NA+ GL  + +K</entry></row><row><entry>Sbjct:</entry><entry>520</entry><entry>VGLLKKGLVGHAPLKLQDLQKASKIYCINALYGLVEVKIK</entry><entry>559</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 27&gt; which encodes the amino acid sequence &lt;SEQ ID 28&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00039" num="00039"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.2669 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00040" num="00040"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 303/572 (52%), Positives = 406/572 (70%), Gaps = 1/572 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MHIETVIDFKELGKRYRFKNPTKELIADTLEQVLEVIKEVDYYQSQNYYVVGYLSYEASA</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MH +T+IDFKELG+RY F  P  EL+A +L+QV  VI++V +YQ   YYVVGYLSYEA+A</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>MHRKTIIDFKELGQRYLFDEPLVELVAKSLDQVGPVIEKVQHYQQLGYYVVGYLSYEAAA</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>AFDSHFKVSQQKLAGEHLAYFTVHKDCENEAFPLSYENVRLADNWTANVSEQEYQEAIAN</entry><entry>120</entry></row><row><entry /><entry /><entry> FD+  +    +L  E+LAYFTVHK C+ +  PL Y+++ + + W +   ++ YQ+AI</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>FFDNALQTHNDRLGNEYLAYFTVHKTCQKKDLPLDYDSITIPNQWVSATQKEAYQKAIET</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IKGQIRQGNTYQVNYTLELSQQL-CSDPFSVYERLMVEQGAGYNAYIAYDDKRILSVSPE</entry><entry>179</entry></row><row><entry /><entry /><entry>I  +++QGNTYQVNYTL+L+Q+L  +D  ++Y +L+VEQ AGYNAYIA+D+  ++S SPE</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>IHREMQQGNTYQVNYTLQLTQELNAADSLAIYNKLVVEQAAGYNAYIAHDEFAVISASPE</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>LFFKKKDEVLTTRPMKGTSARKPTYQEDVAERDWLANDPKNRSENMMIVDLLRNDMGRIC</entry><entry>239</entry></row><row><entry /><entry /><entry>LFFK++   LTTRPMKGT+ R      D  E DWL  D KNRSENMMIVDLLRNDMG+IC</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>LFFKQEGNRLTTRPMKGTTKRGVNSWLDQQEHDWLQADGKNRSENMMIVDLLRNDMGKIC</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>DVGTVKVKKLCQVEQYATVWQMTSTIEGVLSPEVTLMSIFQALYPCGSITGAPKISTMAI</entry><entry>299</entry></row><row><entry /><entry /><entry>  G+V+V +LC+VE+Y+TVWQMTSTI G L  +  L+ I +AL+PCGSITGAPK+STMAI</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>QTGSVRVDRLCEVERYSTVWQMTSTIVGDLKADCDLIDILKALFPCGSITGAPKVSTMAI</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>INELEKRPRGIYCGTIGLCMPDGQAIFNVPIRTVQMKGQQAYYGVGGGITWESQTDSEYE</entry><entry>359</entry></row><row><entry /><entry /><entry>I  LE +PRGIYCG+IG+C+PDG+  FNVPIRT+Q+   QA YGVGGGITW+S+ + EYE</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>ITSLEPKPRGIYCGSIGICLPDGRRFFNVPIRTIQLSHNQATYGVGGGITWQSKWEDEYE</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>ETRQKSAVLTRVNPKFQLITTGRVTENKLLFSQQHVERLVESASYFAYSFDKSKFERELK</entry><entry>419</entry></row><row><entry /><entry /><entry>E  QK+A L R    F L TT +V   K+ F +QH+ RL E+A+YFAY +++   +++L</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>EVHQKTAFLYRHKQIFDLKTTAKVEHKKIAFLEQHLNRLKEAATYFAYPYNEKALQKQLS</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>420</entry><entry>KYLHQLDEKDYRLKIMLDKTGKVTFEVKQLVNLSKKFLTAEVVVQDYPIKLSPFTYFKTS</entry><entry>479</entry></row><row><entry /><entry /><entry> YL   +   YRL I L K GK++   + L  LS  FLTA++ +Q   +  SPFTYFKTS</entry></row><row><entry>Sbjct:</entry><entry>423</entry><entry>TYLENKNNAAYRLMIRLSKDGKISLSDQPLEPLSADFLTAQLSLQKKDVTASPFTYFKTS</entry><entry>482</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>YRPHIIEGQNEKIFVSPEGLLLETSIGNIVLEKNGRFLTPDLSEGGLNGIYRRHLLKNQK</entry><entry>539</entry></row><row><entry /><entry /><entry>YRPHI +   E++F +  G LLETSIGN+ ++      TP ++ G L G++R+ LL   +</entry></row><row><entry>Sbjct:</entry><entry>483</entry><entry>YRPHIEQKSYEQLFYNQAGQLLETSIGNLFVQLGQTLYTPPVAVGILPGLFRQELLATGQ</entry><entry>542</entry></row><row><entry /></row><row><entry>Query:</entry><entry>540</entry><entry>VIEAPLTLKDLESADAIYACNAVRGLYPLNLK</entry><entry>571</entry></row><row><entry /><entry /><entry>  E  +TL DL+ A AI+  NAVRGLYPLNL+</entry></row><row><entry>Sbjct:</entry><entry>543</entry><entry>AQEKEVTLADLKEASAIFGGNAVRGLYPLNLE</entry><entry>574</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 13

A DNA sequence (GBSx0010) was identified in <i>S. agalactiae </i>&lt;SEQ ID 29&gt; which encodes the amino acid sequence &lt;SEQ ID 30&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00041" num="00041"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1564(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 31&gt; which encodes the amino acid sequence &lt;SEQ ID 32&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00042" num="00042"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5335(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00043" num="00043"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 220/267 (82%), Positives = 243/267 (90%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>10</entry><entry>LLLEITKIARATYYYQLKKLNKPNKDKAIKSDIQSIYDEHRGNYGYRRIYLELRNRGFVI</entry><entry>69</entry><entry /></row><row><entry /><entry /><entry>+LLEI  ++R+TYYYQ+K+L + +KD  +K  I+ IYDEH+GNYGYRRI++ELRNRGFV+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLLEILDLSRSTYYYQVKRLAQGDKDIELKHVIREIYDEHKGNYGYRRIHMELRNRGFVV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>70</entry><entry>NHKRVQGLMKSMGLTARIRRKRKYASYKGEVGKKADNLIQRQFEGSKPYEKCYTDVTEFA</entry><entry>129</entry></row><row><entry /><entry /><entry>NHK+VQ LMK MGL ARIRRKRKY+SYKGEVGKKADNLI+R FEGSKPYEKCYTDVTE A</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>NHKKVQRLMKVMGLAARIRRKRKYSSYKGEVGKKADNLIKRHFEGSKPYEKCYTDVTELA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>130</entry><entry>LPEGKLYLSPVLDGYNSEIIDFTLSRSPDLKQVQTMLEBAFPAASYSETILHSDQGWQYQ</entry><entry>189</entry></row><row><entry /><entry /><entry>LPEGKLYLSPVLDGYNSEIIDFTLSRSP+LKQVQTMLE+ FPA SYS TILHSDQGWQYQ</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LPEGKLYLSPVLDGYNSEIIDFTLSRSPNLKQVQTMLEKTFPADSYSGTILHSDQGWQYQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>190</entry><entry>HKSYHQFLEDKGIRPSMSRKGNSPDNGMMESFFGILKSEMFYGLEKSYKSLDDLEQAITD</entry><entry>249</entry></row><row><entry /><entry /><entry>H+SYH FLE KGI  SMSRKGNSPDNGMMESFFGILKSEMFYGLE +Y+SLD LE+AITD</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>HQSYHDFLESKGILASMSRKGNSPDNGMMESFFGILKSEMFYGLETTYQSLDKLEEAITD</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>250</entry><entry>YIFYYNNKRIKAKLKGLSPVQYRTKSF</entry><entry>276</entry></row><row><entry /><entry /><entry>YIFYYNNKRIKAKLKG SPVQYRTKSF</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YIFYYNNKRIKAKLKGFSPVQYRTKSF</entry><entry>267</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 14

A DNA sequence (GBSx0011; GBSx2234) was identified in <i>S. agalactiae </i>&lt;SEQ ID 33&gt; which encodes the amino acid sequence &lt;SEQ ID 34&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00044" num="00044"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3578(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 35&gt; which encodes the amino acid sequence &lt;SEQ ID 36&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00045" num="00045"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3869(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00046" num="00046"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 107/170 (62%), Positives = 134/170 (77%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKLSYEDKLEIYELRKIGMSWSQISQRYDVRISNLKYMIKLMDRYGVEIVEKGRNEYYPP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MK + E K++IYELR++G S   IS+++D+  S+LKYMI+L+DRYGV IV+K +N YY P</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKFNQETKVKIYELRQMGESIKSISKKFDMAESDLKYMIRLIDRYGVTIVQKCKNHYYSP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>ELKQEMIDKVLIHGCSQLSVSLDYALSNCSILTNWLSQFKKNGYTIVEKTRGRPSKMGRK</entry><entry>120</entry></row><row><entry /><entry /><entry>ELKQE+I+KVLI G SQ   SLDYAL   S+L+ W++Q+KKNGYTI+EK RGRPSKMGRK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ELKQEIINKVLIDGQSQKQTSLDYALPTSSMLSRWIAQYKKNGYTILEKPRGRPSKMGRK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>RKKTWEEMTELERLQEENERLRTENAFLKKLRDLRLRDEALQSERQKQLE</entry><entry>170</entry></row><row><entry /><entry /><entry>RKK  EEMTE+ERLQ+E E  R ENA LKKLR+ RLRDEA   E+QK  +</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>RKKNLEEMTEVERLQKELEYPRAENAVLKKLREYRLRDEAKLKEQQKSFK</entry><entry>170</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 15

A DNA sequence (GBSx0012) was identified in <i>S. agalactiae </i>&lt;SEQ ID 37&gt; which encodes the amino acid sequence &lt;SEQ ID 38&gt;. This protein is predicted to be oxyR protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00047" num="00047"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1323(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10033&gt; which encodes amino acid sequence &lt;SEQ ID 10034&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00048" num="00048"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA91664 GB:Z67753 former trsE (rbcR homolog) [<i>Odontella sinensis</i>]</entry><entry /></row><row><entry>Identities = 72/259 (27%), Positives = 127/259 (48%), Gaps = 7/259 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>QKLMYLESIELYSNITKAAAMLFISQPYLSKVIKQLENELEIKLIQSQGHQTFLTYAGQR</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>Q+L  L++I    + T+AA  LF+SQP LSK IK LE+ L I L+  + +   LT AG+</entry><entry /></row><row><entry>Sbjct:</entry><entry>8</entry><entry>QQLRILKAIATEKSFTRAAEVLFVSQPSLSKQIKTLESRLNISLLNRENNIVSLTQAGKL</entry><entry>67</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>YLFYLKEIDMIERQMAKELYLIRSDKKGEITLGINSGLASSILANVLPKFNLEHPEISVK</entry><entry>124</entry></row><row><entry /><entry /><entry>+L Y + I  +  +  + L  +++  +G + +G +  + + ++  VL  F   HP+I+++</entry><entry /></row><row><entry>Sbjct:</entry><entry>68</entry><entry>FLEYSERILALCEESCRVLNDLKTGDRGNLIVGASQTIGTYLMPRVLALFAQNHPQINIE</entry><entry>127</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LLENNQNISEQLVASGDIDLAV--GMAPILYKDGIASTTIYRDELFLMIPTTSQLYNAEK</entry><entry>182</entry></row><row><entry /><entry /><entry>+  ++     + V  GDID+AV  G  P   +  +       DEL L+IP +      +K</entry><entry /></row><row><entry>Sbjct:</entry><entry>128</entry><entry>VHVDSTRKIAKRVLEGDIDIAVVGGNIPEEIEKNLKVEDFVNDELILIIPKSHPFALKKK</entry><entry>187</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>RGQIIPFEYPISVLD-NEPLILTPLEYGIGKTIAQFYELHHMSLNQMITTSTVPTAASLS</entry><entry>241</entry></row><row><entry /><entry /><entry>+       Y ++ +  N    +  L   I   IA F       + Q+ +   + TA SL</entry><entry /></row><row><entry>Sbjct:</entry><entry>188</entry><entry>KKINKDDLYHLNFITLNSNSTIRKLIDNILIQIA-FEPKQFNIIMQLNSIEAIKTAVSL-</entry><entry>245</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>LSGMGATFVPQTLIHRYLD</entry><entry>260</entry></row><row><entry /><entry /><entry>  G+GA FV  + I + ++</entry><entry /></row><row><entry>Sbjct:</entry><entry>246</entry><entry>--GLGAAFVSSSAIEKEIE</entry><entry>262</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 39&gt; which encodes the amino acid sequence &lt;SEQ ID 40&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00049" num="00049"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="14pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.28</entry><entry>Transmembrane</entry><entry>109-125 (109-126)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.27</entry><entry>Transmembrane</entry><entry>146-162 (146-162)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1510(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00050" num="00050"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC22434 GB:U32761 transcriptional regulator [<i>Haemophilus</i></entry><entry /></row><row><entry><i>influenzae </i>Rd]</entry></row><row><entry>Identities = 157/303 (51%), Positives = 221/303 (72%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>IRQGESYLDIKQIRYFIAIVENHFNLSQAAELLYVSQPTLSMMINDFEKRENVKLFKRKR</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+ +G   +DI+ +RYF++IV+N FNLS+A++ LYVSQP LSMMI +FE REN+++FKR</entry><entry /></row><row><entry>Sbjct:</entry><entry>9</entry><entry>VLRGVKMMDIRHLRYFVSIVDNDFNLSRASQNLYVSQPALSMMITEFENRENIQIFKRAS</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>GRIIGLTYLGDNYYKDAQKVLSLYDDMFLKLHDHSKGLKGSINIGIPPLILSVVFSEVMP</entry><entry>121</entry></row><row><entry /><entry /><entry>G+IIGLT+ G+NYY+DA++V+  Y+DM   L+      KG+I IGIPPL+LS VFS V+P</entry><entry /></row><row><entry>Sbjct:</entry><entry>69</entry><entry>GKIIGLTFAGENYYRDAKEVIKRYNDMRTNLYKSKDCKKGTITIGIPPLVLSAVFSSVLP</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>KLILENPGIQFNVKEIGAYQLKNELLVGNVDVAVLLSPTGIADNLVETYEIQRSELSVCL</entry><entry>181</entry></row><row><entry /><entry /><entry> LIL+NP I F +KEIGAY LK+ELL+  VD+AVLL P  I+ N++++ EI  SEL++ L</entry><entry /></row><row><entry>Sbjct:</entry><entry>129</entry><entry>HLILKNPDINFIIKEIGAYALKSELLLDKVDLAVLLYPERISKNIIDSIEIHSSELALFL</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>SPRHRLASKKVIQWEDLTDEQLALFDPSFMVHHLVLEACERHQVRPNIILTSSSWDFMLN</entry><entry>241</entry></row><row><entry /><entry /><entry>SP+H LA K+ I W DL  +++A+FD +FM+HH + EA ER+   P+I+L SS WDF+L+</entry><entry /></row><row><entry>Sbjct:</entry><entry>189</entry><entry>SPKHVLAKKQQITWADLHQQKMAIFDQTFMIHHHLKEAFERNNCYPDIVLDSSCWDFLLS</entry><entry>248</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>STKINHNVLTICPKPITELYQLKDIKCIPMERPISWRVVLTRLRKKSYSEIEAYIMDDLL</entry><entry>301</entry></row><row><entry /><entry /><entry>+ K N  +LTI P P+ ELY  K+  C  +E P+ W+V L R RK  Y+ +E YI D LL</entry><entry /></row><row><entry>Sbjct:</entry><entry>249</entry><entry>AVKTNKELLTILPLPMAELYHSKEFLCRKIESPVPWKVTLCRQRKTVYTHLEEYIFDKLL</entry><entry>308</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>QSF</entry><entry>304</entry></row><row><entry /><entry /><entry>++F</entry><entry /></row><row><entry>Sbjct:</entry><entry>309</entry><entry>EAF</entry><entry>311</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00051" num="00051"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 61/227 (26%), Positives = 111/227 (48%), Gaps = 10/227 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>9</entry><entry>YLESIELYSNITKAAAHLFISQPYLSKVIKQLENELEIKLIQ-SQGHQTFLTYAGQRYLF</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>++  +E + N+++AA  L++SQP LS +I   E    +KL +  +G    LTY G  Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>17</entry><entry>FIAIVENHFNLSQAAELLYVSQPTLSDMMINDFEKRENVKLFKRKRGRIIGLTYLGDNYYK</entry><entry>76</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>YLKEIDMIERQMAKELYLIRSDKKGEITLGINSGLASSILANVLPKFNLEHPEISVKLLE</entry><entry>127</entry></row><row><entry /><entry /><entry>  +++  +   M  +L+      KG I +GI   + S + + V+PK  LE+P I   + E</entry><entry /></row><row><entry>Sbjct:</entry><entry>77</entry><entry>DAQKVLSLYDDMFLKLHDHSKGLKGSINIGIPPLILSVVFSEVMPKLILENPGIQFNVKE</entry><entry>136</entry></row><row><entry /></row><row><entry>Query:</entry><entry>128</entry><entry>NNQNISEQLVASGDIDLAVGMAPILYKDGIAST-TIYRDELFLMIPTTSQLYNAEKRGQI</entry><entry>186</entry></row><row><entry /><entry /><entry>      +  +  G++D+AV ++P    D +  T  I R EL + +    +L  A K+  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>137</entry><entry>IGAYQLKNELLVGNVDVAVLLSPTGIADNLVETYEIQRSELSVCLSPRHRL--ASKK--V</entry><entry>192</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>IPFEYPISVLDNEPLILTPLEYGIGKTIAQFYELHHMSLNQMITTST</entry><entry>233</entry></row><row><entry /><entry /><entry>I +E     L +E L L    + +   + +  E H +  N ++T+S+</entry><entry /></row><row><entry>Sbjct:</entry><entry>193</entry><entry>IQWE----DLTDEQLALFDPSFMVHHLVLEACERHQVRPNIILTSSS</entry><entry>235</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 16

A DNA sequence (GBSx0013) was identified in <i>S. agalactiae </i>&lt;SEQ ID 41&gt; which encodes the amino acid sequence &lt;SEQ ID 42&gt;. This protein is predicted to be aminoacylase (cpsA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00052" num="00052"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.75</entry><entry>Transmembrane</entry><entry>385-401 (385-401)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1298(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00053" num="00053"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF36227 GB: AF168363 aminoacylase [<i>Lactococcus lactis</i>]</entry><entry /></row><row><entry>Identities = 201/395 (50%), Positives = 274/395 (68%), Gaps = 5/395 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>LRHQLFEKLDQKCDQMVAIRRYLHENPELSFKETKTAAYISDFYKGKDCHVQTQFGGMNG</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>L + L   L Q  ++M+ IRR+LH+ PE+SF+E +T  YI  FYK  DC  +    G  G</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>LLNNLLTSLTQYENEMIQIRRHLHQYPEISFQEKETFKYIMGFYKELDCEPKLIGKGF-G</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>VVVDIYGDKATDKPIKHIALRADFDALPIQEETGLSFASKTAGVMHACGHDAHTAYLLIL</entry><entry>125</entry></row><row><entry /><entry /><entry>++VDI G K+     K +ALRADFDAL I E+  LSF S   GVMHACGHDAHTAYL++L</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>IIVDIEGGKSG----KTLALRADFDALAIFEDNDLSFKSVNPGVMHACGHDAHTAYLMVL</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>AESLIELKSEFSGHIRILHQPAEEVPPGGAKAMIEAGCLDGIDAVLGIHVMSTMEEGTVQ</entry><entry>185</entry></row><row><entry /><entry /><entry>A  L+++K E  G +RI+HQPAEEV PGGAK+MI+AG LDG+D ++G+HVM+T++ G +</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>ARELVKIKQELPGRVRIVHQPAEEVSPGGAKSMIKAGALDGVDNMIGVHVMTTIKTGVIA</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>YHAGPIQTGRATFKVILQGKGGHGSMPHRANDTIVAASSFVMAAQTIVSRRVNPFDTAVV</entry><entry>245</entry></row><row><entry /><entry /><entry>YH    QTGR+ F + ++G GGH SMP  +ND IVAAS FV   QT++SRR++PFD   V</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>YHNKETQTGRSNFTITIKGNGGHASMPQLSNDAIVAASYFVTELQTVISRRIDPFDMGTV</entry><entry>237</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>TIGSWDGKGSANVIKDSVTLEGDVRVMSEETRGVVEEEFKRILDGIAQTYGVSYQLDYQN</entry><entry>305</entry></row><row><entry /><entry /><entry>TIGSFDG GS N I+D V L+GDVR+M E TR V+ ++ K+I  G  T+GV   +DY +</entry></row><row><entry>Sbjct:</entry><entry>238</entry><entry>TIGSFDGAGSFNAIQDKVLLKGDVRMMKETTRKVIRDQVKQIAKGVGVTFGVEVIVDYDD</entry><entry>297</entry></row><row><entry /></row><row><entry>Query:</entry><entry>306</entry><entry>DYPVLVNNSEVTQKVANSLKSVAIKEILDVIDCDPQTPSEDFAYYAQTIPACFFYVGAHE</entry><entry>365</entry></row><row><entry /><entry /><entry>+YPVL N+  +T  V +SLK   I E+ +++D  PQ PSEDF+YY Q +P+ FFY+GA</entry></row><row><entry>Sbjct:</entry><entry>298</entry><entry>NYPVLFNSENLTHFVVDSLKDQNISEVNNIVDLGPQNPSEDFSYYGQVVPSTFFYIGAQP</entry><entry>357</entry></row><row><entry /></row><row><entry>Query:</entry><entry>366</entry><entry>EGQPYYPHHHPKFQIAESSLMVSAKSMATAALAML</entry><entry>400</entry></row><row><entry /><entry /><entry>E    YPHH P F++ E S++++AK++AT  +  L</entry></row><row><entry>Sbjct:</entry><entry>358</entry><entry>EDGGNYPHHSPLFKMNEKSILIAAKAVATVTINYL</entry><entry>392</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 17

A DNA sequence (GBSx0014) was identified in <i>S. agalactiae </i>&lt;SEQ ID 43&gt; which encodes the amino acid sequence &lt;SEQ ID 44&gt;. This protein is predicted to be drug transporter. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00054" num="00054"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible Site: −1 Crend: 8</entry><entry /></row><row><entry>McG: Discrim Score: 6.19</entry></row><row><entry>GvH: Signal Score (−7.5): −0.899999</entry></row><row><entry>     Possible site: 31</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry>ALOM program count: 11 value: −12.15 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.15</entry><entry>Transmembrane</entry><entry>169-185 (166-190)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.86</entry><entry>Transmembrane</entry><entry>229-245 (224-250)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.65</entry><entry>Transmembrane</entry><entry>  82-98 (78-111)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.60</entry><entry>Transmembrane</entry><entry>436-452 (428-457)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.48</entry><entry>Transmembrane</entry><entry>202-218 (198-222)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry>334-350 (332-352)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.88</entry><entry>Transmembrane</entry><entry>358-374 (354-376)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.09</entry><entry>Transmembrane</entry><entry>301-317 (301-317)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.81</entry><entry>Transmembrane</entry><entry>102-118 (101-119)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.71</entry><entry>Transmembrane</entry><entry>  52-68 (50-70)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.70</entry><entry>Transmembrane</entry><entry>271-287 (270-288)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 0.32</entry><entry>401</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.93</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.5861(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00055" num="00055"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB02058 GB: Z79702 hypothetical protein Rv2333c [<i>Mycobacterium</i></entry><entry /></row><row><entry><i>tuberculosis</i>]</entry></row><row><entry>Identities = 118/405 (29%), Positives = 199/405 (49%), Gaps = 9/405 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>KLLVGIVLAVLSFWLFAQS-ILNMG-PDVQSSLGISSGAMDIGVSSTALFSGLFIVVTGG</entry><entry>70</entry><entry /></row><row><entry /><entry /><entry>+LL  I   +  F +F  + I+N+  PD+Q S  +    +   V+S +L   +FI+</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>QLLTLIATGLGLFMIFLDALIVNVALPDIQRSFAVGEDGLQWVVASYSLGMAVFIMSAAT</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>71</entry><entry>LADKLGRVKFTFIGLCLNIIGSLLIVLANGAVLFIMGRIFQGLAAAFIMPSTMALVKTYY</entry><entry>130</entry></row><row><entry /><entry /><entry>LAD  GR ++  IG+  L  +GS+   LA    +    R  QGL AA +  +++ALV   +</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>LADLDGRRRWYLIGVSLFTLGSIACGLAPSIAVLTTARGAQGLGAAAVSVTSLALVSAAF</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>131</entry><entry>-DGKDRQRAVSFWSIGSWGGSGLCSYFGGAVASTLGWRYVFIFSI-IASVVSFLLILGTP</entry><entry>188</entry></row><row><entry /><entry /><entry>+ K++ RA+  W+  +  G+      GG +    GWR +F  ++ + ++V FL +</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>PEAKEKAPAIGIWTAIASIGTTTGPTLGGLLVDQWGWRSIFYVNLPMGALVLFLTLCYVE</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>189</entry><entry>ESKNVGQRTHFDYLGLIIFIISMLSLNIGISMAQEHGLMNVIPLSLFTVMLIGFVLFYYV</entry><entry>248</entry></row><row><entry /><entry /><entry>ES N  +   FD  G ++FI+++ +L   +    + G  +V  + +     +G  LF ++</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>ESCN-ERARRFDLSGQLLFIVAVGALVYAVIEGPQIGWTSVQTIVMLWTAAVGCALFVWL</entry><entry>243</entry></row><row><entry /></row><row><entry>Query:</entry><entry>249</entry><entry>ETRKSNSFIDFHLFENRFY-LGATISNFLLNAVAGTLIVINTYMQQGRQLTPKVAGEMSL</entry><entry>307</entry></row><row><entry /><entry /><entry>E R SN  +D  LF +  Y L       +  AV G L++   ++Q  R  TP V G M L</entry></row><row><entry>Sbjct:</entry><entry>244</entry><entry>ERRSSNPMMDLTLFRDTSYALAIATICTVFFAVYGMLLLTTQFLQNVRGYTPSVTGLMIL</entry><entry>303</entry></row><row><entry /></row><row><entry>Query:</entry><entry>308</entry><entry>GYLVCVLIAIRVGEKILQRFGARKPMLLGAMSTFVGIFLMTLVNIQGPLYLVLVFVGYAL</entry><entry>367</entry></row><row><entry /><entry /><entry> +   V I   +   ++ R GAR P+L G     +G+ ++     +      LV VG  L</entry></row><row><entry>Sbjct:</entry><entry>304</entry><entry>PFSAAVAIVSPLVGHLVGRIGARVPILAGLCMLMLGLLMLIFSEHRSS---ALVLVGLGL</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>368</entry><entry>FGTGLGIYATPSTDTAISSIPNEKVGSASGIYKMASSLGGAIGVA</entry><entry>412</entry></row><row><entry /><entry /><entry> G+G+ +  TP T  A++++P E+ G ASGI     ++G  IG A</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>CGSGVALCLTPITTVAMTAVPAERAGMASGIMSAQRAIGSTIGFA</entry><entry>405</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 45&gt; which encodes the amino acid sequence &lt;SEQ ID 46&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00056" num="00056"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.28</entry><entry>Transmembrane</entry><entry>169-185 (165-189)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.23</entry><entry>Transmembrane</entry><entry>  12-28 (11-32)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.17</entry><entry>Transmembrane</entry><entry>429-445 (423-450)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.64</entry><entry>Transmembrane</entry><entry>203-219 (200-222)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.41</entry><entry>Transmembrane</entry><entry>227-243 (225-245)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.72</entry><entry>Transmembrane</entry><entry>  82-98 (80-99)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.72</entry><entry>Transmembrane</entry><entry>136-152 (135-155)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.92</entry><entry>Transmembrane</entry><entry>302-318 (299-319)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.55</entry><entry>Transmembrane</entry><entry>261-277 (261-277)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.07</entry><entry>Transmembrane</entry><entry>331-347 (331-347)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.06</entry><entry>Transmembrane</entry><entry>  56-72 (56-72)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.96</entry><entry>Transmembrane</entry><entry>351-367 (351-368)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.37</entry><entry>Transmembrane</entry><entry>104-120 (103-120)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4312(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00057" num="00057"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>!GB: AJ250422 ORFC [<i>Oenococcus oeni</i>] 271 1e−71</entry><entry /></row><row><entry>Identities = 152/445 (34%), Positives = 248/445 (55%), Gaps = 7/445 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSHHQQTVSKQTIMAIIAIALIGFSGILSETSMNVTFPTLMSVYQLPLNSLQWMTTIYLL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M    Q VS    +AI+ +A + F G+L ETSMNVTFPTLM  + + LN +QW+TT YLL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MQKDNQPVSLHVKLAILGLAGLAFCGVLIETSMNVTFPTLMQQFSISLNKVQWLTTAYLL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>AVAIMMTTSATLKKNVRERPLFFMATGLFTFGTILAVLTQSFAIMLLARIFQGIGTGLVM</entry><entry>120</entry></row><row><entry /><entry /><entry> VA  ++ +A ++K    + +FF A  LF  G I + L  +F I+L+ R+ Q + TGL +</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LVAATISIAAFIEKRFIFKKIFFWAGLLFIIGVICSALAPNFLILLIGRLIQALSTGLAI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>PQMFNIILERVPMHKVGLFMGFAGLIISLAPAFGPTYGGFMISHFSWQWIFICILPVPLI</entry><entry>180</entry></row><row><entry /><entry /><entry>P +   I++++P  K G +M     ++   P+ GPTYGG +    SW+ IF  +LP+ LI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PLLITEIMQQIPQKKQGSYMELVEWLLLWQPSLGPTYGGVITQDLSWRLIFWFVLPIGLI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>AGILAYYYLEDSPVSEKVPFDWLAFIALSISLTSALLAITSLE-NGSVNLYYLGLFILSF</entry><entry>239</entry></row><row><entry /><entry /><entry>A ++   ++E      K+PF W  FI+L ++L S  +A+ +    G  ++ + G  +++</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>AWLIGLSFIEQKSSPSKIPFAWKQFISLILALLSITVAVNNAGIYGWTSIKFYGFLLIAV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>IL---FLYKNLTAKQPFLDIRILKIPSLTFGLIPFFVFQLINLGINFLTPNFIVMEKIAN</entry><entry>296</entry></row><row><entry /><entry /><entry>IL   F+  +  ++Q  + I I K       L+ +F+ Q I L + FL PN+  +</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>ILLIVFIKLSTNSRQALISISIFKKWEFVCPLLIYFLIQFIQLSLTFLLPNYAQLILKKG</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>297</entry><entry>SSQAGMVLLPGTLLGALLAPAFGKLYDQKGARLSLYLGNALFSLSLIIMTLQTRHFMLLP</entry><entry>356</entry></row><row><entry /><entry /><entry>   +G++LL G+L+ A+L P  G++ D    ++ L +G      S I  T+  R+  +</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>VMISGIMLLCGSLISAILQPLTGRMLDSFSVKIPLVIGAFFLITSTISFTIFQRYLSVFL</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>357</entry><entry>FTLLYILFTFGRNMGFNNSLATAIRELPAEKNADATAIFQMMQQFAGALGTAMAS-LIAN</entry><entry>415</entry></row><row><entry /><entry /><entry>   LY+++  G +  FNNSL  A+++LP +  +D  A+F  +QQ+AG+LGT++AS L+AN</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>IAALYVIYMIGFSFVFNNSLTYALQKLPLKLISDGNAVFNTLQQYAGSLGTSVASALLAN</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>SQAEFTSGVQSVYLLFTIFALLDFI</entry><entry>440</entry></row><row><entry /><entry /><entry>     T G QS Y       +L+FI</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>GIG--TDGKQSNYTGSRHIFILNFI</entry><entry>443</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00058" num="00058"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 91/369 (24%), Positives = 160/369 (42%), Gaps = 14/369 (3%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>82</entry><entry>FIGLCLNIIGSLLIVLANGAVLFIMGRIFQGLAAAFIMPSTMALVKTYYDGKDRQRAVSF</entry><entry>141</entry><entry /></row><row><entry /><entry /><entry>F+   L   G++L VL     + ++ RIFQG+    +MP    ++            + F</entry></row><row><entry>Sbjct:</entry><entry>83</entry><entry>FMATGLFTFGTILAVLTQSFAIMLLARIFQGIGTGLVMPQMFNIILERVPMHKVGLFMGF</entry><entry>142</entry></row><row><entry /></row><row><entry>Query:</entry><entry>142</entry><entry>WSIGSWGGSGLCSYFGGAVASTLGWRYVFIFSIIASVVSFLLILGTPESKNVGQKTHFDY</entry><entry>201</entry></row><row><entry /><entry /><entry>  +           +GG + S   W+++FI  +   +++ +L     E   V +K  FD+</entry></row><row><entry>Sbjct:</entry><entry>143</entry><entry>AGLIISLAPAFGPTYGGFMISHFSWQWIFICILPVPLIAGILAYYYLEDSPVSEKVPFDW</entry><entry>202</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>LGLIIFIISMLSLNIGISMAQEHGLMNVIPLSLFTVMLIGFVLFYYVETRKSNSFIDFHL</entry><entry>261</entry></row><row><entry /><entry /><entry>L  I   IS+ S  + I+ + E+G +N+  L LF   ++ F+LF Y        F+D  +</entry></row><row><entry>Sbjct:</entry><entry>203</entry><entry>LAFIALSISLTSALLAIT-SLENGSVNLYYLGLF---ILSFILFLYKNLTAKQPFLDIRI</entry><entry>258</entry></row><row><entry /></row><row><entry>Query:</entry><entry>262</entry><entry>FENRFYLGATISNFLLNAV-AGTLIVINTYMQQGRQLTPKVAGEMSL-GYLVCVLIAIRV</entry><entry>319</entry></row><row><entry /><entry /><entry> +        I  F+   +  G   +   ++   +      AG + L G L+  L+A</entry></row><row><entry>Sbjct:</entry><entry>259</entry><entry>LKIPSLTFGLIPFFVFQLINLGINFLTPNFIVMEKIANSSQAGMVLLPGTLLGALLAPAF</entry><entry>318</entry></row><row><entry /></row><row><entry>Query:</entry><entry>320</entry><entry>GEKILQRFGARKPMLLGAMSTFVGIFLMTLVNIQGPLYLVLVF-VGYALFGTGLGIYATP</entry><entry>378</entry></row><row><entry /><entry /><entry>G K+  + GAR  + LG     + + +MTL   Q   +++L F + Y LF  G  +</entry></row><row><entry>Sbjct:</entry><entry>319</entry><entry>G-KLYDQKGARLSLYLGNALFSLSLIIMTL---QTRHFMLLPFTLLYILFTFGRNMGFNN</entry><entry>374</entry></row><row><entry /></row><row><entry>Query:</entry><entry>379</entry><entry>STDTAISSIPNEKVGSASGIYKMASSLGGAIGVATSIAIYHAFSGNADFHKAALCGLILN</entry><entry>438</entry></row><row><entry /><entry /><entry>S  TAI  +P EK   A+ I++M     GA+G A +  I ++    A+F        +L</entry></row><row><entry>Sbjct:</entry><entry>375</entry><entry>SLATAIRELPAEKNADATAIFQMMQQFAGALGTAMASLIANS---QAEFTSGVQSVYLLF</entry><entry>431</entry></row><row><entry /></row><row><entry>Query:</entry><entry>439</entry><entry>LVFCSLSIL</entry><entry>447</entry></row><row><entry /><entry /><entry> +F  L  +</entry></row><row><entry>Sbjct:</entry><entry>432</entry><entry>TIFALLDFI</entry><entry>440</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 18

A DNA sequence (GBSx0015) was identified in <i>S. agalactiae </i>&lt;SEQ ID 47&gt; which encodes the amino acid sequence &lt;SEQ ID 48&gt;. This protein is predicted to be transposase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00059" num="00059"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3116(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 19

A DNA sequence (GBSx0016) was identified in <i>S. agalactiae </i>&lt;SEQ ID 49&gt; which encodes the amino acid sequence &lt;SEQ ID 50&gt;. This protein is predicted to be L11 protein (rplK). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00060" num="00060"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1859(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00061" num="00061"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA53739 GB: X76134 L11 protein [<i>Staphylococcus carnosus</i>]</entry><entry /></row><row><entry>Identities = 117/139 (84%), Positives = 129/139 (92%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAKKVEK+VKLQIPAGKA PAPPVGPALGQAG+NIMGF KEFNART +QAG+IIPV ISV</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAKKVEKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTQEQAGLIIPVEISV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YEDKSFDFITKTPPAAVLLKKAAGVEKGSGEPNKTKVATITRAQVQEIAETKMPDLNAAN</entry><entry>120</entry></row><row><entry /><entry /><entry>YED+SF FITKTPPA VLLKKAAGVEKGSGEPNK KVAT+T+ QV+EIA+TKMPDLNAA+</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YEDRSFTFITKTPPAPVLLKKAAGVEKGSGEPNKNKVATVTKDQVREIAQTKMPDLNAAD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>LESAMRMIEGTARSMGFTV</entry><entry>139</entry></row><row><entry /><entry /><entry> E+AMR+IEGTARSMG TV</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>EEAAMRIIEGTARSMGITV</entry><entry>139</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 51&gt; which encodes the amino acid sequence &lt;SEQ ID 52&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00062" num="00062"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4276(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00063" num="00063"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 136/141 (96%), Positives = 139/141 (98%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV</entry><entry /></row><row><entry>Sbjct:</entry><entry>25</entry><entry>MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV</entry><entry>84</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YEDKSFDFITKTPPAAVLLKKAAGVEKGSGEPNKTKVATITRAQVQEIAETKMPDLNAAN</entry><entry>120</entry></row><row><entry /><entry /><entry>YEDKSFDFITKTPPAAVLLKKAAGVEKGSG PN TKVAT+TRAQVQEIAETKMPDLNAAN</entry><entry /></row><row><entry>Sbjct:</entry><entry>85</entry><entry>YEDKSFDFITKTPPAAVLLKKAAGVEKGSGTPNTTKVATVTRAQVQEIAETKNPDLNAAN</entry><entry>144</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>LESAMRMIEGTARSMGFTVTD</entry><entry>141</entry></row><row><entry /><entry /><entry>+E+AMRMIEGTARSMGFTVTD</entry><entry /></row><row><entry>Sbjct:</entry><entry>145</entry><entry>IEAAMRMIEGTARSMGFTVTD</entry><entry>165</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 20

A DNA sequence (GBSx0017) was identified in <i>S. agalactiae </i>&lt;SEQ ID 53&gt; which encodes the amino acid sequence &lt;SEQ ID 54&gt;. This protein is predicted to be ribosomal protein L1 (rplA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00064" num="00064"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2285(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00065" num="00065"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB11879 GB:Z99104 ribosomal protein L1 (BL1) [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 144/228 (63%), Positives = 177/228 (77%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAKKSKNLRAALEKIDSTKAYSVEEAVALAKETNFAKFDATVEVSYNLNIDVKKADQQIR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAKK K    A + +D +KAY V EAVAL K+TN AKFDATVEV++ L +D  K  QQIR</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAKKGKKYVEAAKLVDHSKAYDVSEAVALVKKTNTAKFDATVEVAFRLGVDPSKNHQQIR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GAMVLPAGTGKTSRVLVFARGAKAEEAKAAGADFVGEDDLVAKIQGGWLDFDVVIATPDM</entry><entry>120</entry></row><row><entry /><entry /><entry>GA+VLP GTGKT RVLVFA+G KA+EA+AAGADFVG+ D + KIQ GW DFDV++ATPDM</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GAVVLPNGTGKTQRVLVFAKGEKAKEAEAAGADFVGDTDYINKIQQGWFDFDVIVATPDM</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>MALVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF</entry><entry>180</entry></row><row><entry /><entry /><entry>M  VG++GRVLGP+ LMPNPKTGTVT +V KA+ E K GK+ YR DKAGN+   IGKVSF</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>MGEVGKIGRVLGPKGLMPNPKTGTVTFEVEKAIGEIKAGKVEYRVDKAGNIHVPIGKVSF</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>DDAKLVDNFKAFNDVIVKAKPATAKGTYITNLSITTTQGVGIKVDPNS</entry><entry>228</entry></row><row><entry /><entry /><entry>+D KLV+NF    D I+KAKPA AKG Y+ N+++T+T G G+KVD ++</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>EDEKLVENFTTMYDTILKAKPAAAKGVYVKNVAVTSTMGPGVKVDSST</entry><entry>228</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 55&gt; which encodes the amino acid sequence &lt;SEQ ID 56&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00066" num="00066"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2309(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00067" num="00067"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 208/229 (90%), Positives = 220/229 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAKKSKNLRAALEKIDSTKAYSVEEAVALAKETNFAKFDATVEVSYNLNIDVKKADQQIR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAKKSK +RAALEK+DSTKAYSVEEAVAL KETNFAKFDA+VEV+YNLNIDV+KADQQIR</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAKKSKQMRAALEKVDSTKAYSVEEAVALVKETNFAKFDASVEVAYNLNIDVRKADQQIR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GAMVLPAGTGKTSRVLVFARGAKAEEAKAAGADFVGEDDLVAKIQGGWLDFDVVIATPDM</entry><entry>120</entry></row><row><entry /><entry /><entry>GAMVLP GTGKT RVLVFARGAKAEEAKAAGADFVGEDDLVAKI GGWLDFDVVIATPDM</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GAMVLPNGTGKTQRVLVFARGAKAEEAKAAGADFVGEDDLVAKINGGWLDFDVVIATPDM</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>MALVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF</entry><entry>180</entry></row><row><entry /><entry /><entry>MA+VGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>MAIVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>DDAKLVDNFKAFNDVIVKAKPATAKGTYITNLSITTTQGVGIKVDPNSL</entry><entry>229</entry></row><row><entry /><entry /><entry>D  KLV+NFKAF+DV+ KAKPATAKGTY+ N+SIT+TQGVGIKVDPNSL</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>DADKLVENFKAFHDVMAKAKPATAKGTYMANVSITSTQGVGIKVDPNSL</entry><entry>229</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 21

A DNA sequence (GBSx0018) was identified in <i>S. agalactiae </i>&lt;SEQ ID 57&gt; which encodes the amino acid sequence &lt;SEQ ID 58&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00068" num="00068"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10029&gt; which encodes amino acid sequence &lt;SEQ ID 10030&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00069" num="00069"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB04286 GB:AP001509 nickel transport system (nickel-binding</entry><entry /></row><row><entry>protein) [<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 209/541 (38%), Positives = 324/541 (59%), Gaps = 14/541 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>RRNILLSITCLLMVTLTACHSQDS----KSHKLNSDK-LTLAWGEDFGDVNPHRYNPDQF</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>R+ ILL +  L+   L  C   +S       + N++K +T +W  D G +NPH YNP Q</entry><entry /></row><row><entry>Sbjct:</entry><entry>6</entry><entry>RKLILLFVISLISSILVGCAESESGTVSNEGEENTEKSITFSWPRDIGPMNPHVYNPSQL</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>VIQDMVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA-KYSDGSNFNAANVKRN</entry><entry>118</entry></row><row><entry /><entry /><entry>  Q M+YE LV Y + G+++P LA SW+IS+DGK YTFKLR   ++SDG+ FNA  VK+N</entry><entry /></row><row><entry>Sbjct:</entry><entry>66</entry><entry>FAQSMIYEPLVSYTEGGELQPHLADSWTISEDGKEYTFKLREGVQFSDGTPFNAEIVKKN</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>FDSIFSKSNRGNHNWFNLTNQLENYRALNQSTFEIKLKQAYSATLYDLSMIRPIRFLSDS</entry><entry>178</entry></row><row><entry /><entry /><entry>FD+    S+   H+W  + N LE    +++ TF++ LK+ Y   L DL+++RP+RFL ++</entry><entry /></row><row><entry>Sbjct:</entry><entry>126</entry><entry>FDTWIEHSSL--HSWLGVMNVLEKTEVVDEFTFKMVLKEPYYPALQDLAVVRPVRFLGEA</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>179</entry><entry>AFPKGDDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNENYWGKKPKLKEVTVKVIPDAQ</entry><entry>238</entry></row><row><entry /><entry /><entry> FP   DT++  +K+PIGTG W++   KQ+EY  F RN NYWG+ PK+ +VTVK+IPDA+</entry><entry /></row><row><entry>Sbjct:</entry><entry>184</entry><entry>GFPDDGDTSQ-GIKEPIGTGPWMLSDYKQDEYAVFTRNPNYWGESPKIDKVTVKIIPDAE</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>239</entry><entry>TRALAFESGDVDLIYGNGIIGLDTFAQYTKDKKYVTAISQPMSTRLLLLNAKESIFQDKK</entry><entry>298</entry></row><row><entry /><entry /><entry>TR LAFESG++DLI+G G+I +D F Q  +  +Y T +S+P+ TR LLLN       D +</entry><entry /></row><row><entry>Sbjct:</entry><entry>243</entry><entry>TRVLAFESGELDLIFGEGVISMDAFNQLKESGQYGTDLSEPVGTRSLLLNTSNEKLADLR</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>299</entry><entry>VRQAMNHAIDKVSIAKNTFRGTEKPADTIFSKSTSHSDAKLNPYSYNVDKANQLLDQAGW</entry><entry>358</entry></row><row><entry /><entry /><entry>VR A++H  +K ++ +    G E+ AD I S +  ++D  + P  Y+V++AN  LD+AGW</entry><entry /></row><row><entry>Sbjct:</entry><entry>303</entry><entry>VRLALHHGFNKQAMVEGVTLGLEEKADNILSTNFPYTDIDVEPIEYDVEQANAYLDEAGW</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>359</entry><entry>KMGKDK-VREKDGKTLTLRLPYIATKATDKDLVTYFQGEWRKIGINVSLIAMEEDDYWAN</entry><entry>417</entry></row><row><entry /><entry /><entry>++   K VREK+G+ L L L Y  T    K +    Q EW  IG+ + +  +E</entry><entry /></row><row><entry>Sbjct:</entry><entry>363</entry><entry>ELPAGKTVREKNGEQLELELIYDKTDPLQKAMAETMQAEWAAIGVKLDITGLELTTQIQR</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>418</entry><entry>AKKGNFDMMLTYSWGAPWDPHAWMSALTAKADHGHPENIALENLATKTEMDRLIKSALVD</entry><entry>477</entry></row><row><entry /><entry /><entry> + G+FD+   Y++GAP+DPH++++ + A+A  G  E  A  NL+ K E+D  +++ L</entry><entry /></row><row><entry>Sbjct:</entry><entry>423</entry><entry>RRAGDFDVDFWYNYGAPYDPHSFIN-VVAEAGWGVAE--AHSNLSMKEELDEQVRATLAS</entry><entry>479</entry></row><row><entry /></row><row><entry>Query:</entry><entry>478</entry><entry>PKEENVDRDYKKVLELLHDEAVYIPLTYQSVISVYRKGDFKTMRFAPEENSFPLRYIEKNN</entry><entry>538</entry></row><row><entry /><entry /><entry>  E      Y  +L  L +++V++P++Y     VY++ +     F    +  P   I+ +N</entry><entry /></row><row><entry>Sbjct:</entry><entry>480</entry><entry>TDETERQELYGSILNTLQEQSVFVPISYIKKTVVYQE-NVNEFIFPANRDEHPFNGIDVSN</entry><entry>539</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 59&gt; which encodes the amino acid sequence &lt;SEQ ID 60&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00070" num="00070"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="357pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00071" num="00071"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 131/497 (26%), Positives = 220/497 (43%),</entry><entry /></row><row><entry>Gaps = 55/497 (11%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>ILLSITCLLMVTLTACHSQDSKSHKLN-----SDKLTLAWGEDFGDVNPHRYNP-DQFVI</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>I L +T L++V   AC  Q  ++ +        D+L ++ G       PH ++P D++ +</entry><entry /></row><row><entry>Sbjct:</entry><entry>13</entry><entry>ITLFLTGLILV---ACQQQKPQTKERQRKQRPKDELVVSMGAKL----PHEFDPKDRYGV</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>QD---MVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA-KYSDGSNFNAANVKR</entry><entry>117</entry></row><row><entry /><entry /><entry> +   + +  L++      I+  LAK++ +S+DG T++F L +  K+S+G    A +VK</entry><entry /></row><row><entry>Sbjct:</entry><entry>66</entry><entry>HNEGNITHSTLLKRSPELDIKGELAKTYHLSEDGLTWSFDLHDDFKFSNGEPVTADDVKF</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>NFDSIFSKSNRGNHNWFNLTNQLENYRALNQSTFEIKLKQAYSATLYDLSMIRPIRFLSD</entry><entry>177</entry></row><row><entry /><entry /><entry> +D +     + +   ++LT  ++N   + ++   I L +A+S     L+ I PI</entry><entry /></row><row><entry>Sbjct:</entry><entry>126</entry><entry>TYDML-----KADGKAWDLTF-IKNVEVVGKNQVNIHLTEAHSTFTAQLTEI-PI-----</entry><entry>173</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>SAFPKG--DDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNENYWGKKPKLKEVTVKVIP</entry><entry>235</entry></row><row><entry /><entry /><entry>   PK   +D  K N   PIG+G ++VK  K  E   F RN  + GKKP  K+ T  V+</entry><entry /></row><row><entry>Sbjct:</entry><entry>174</entry><entry>--VPKKHYNDKYKSN---PIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWT-WVLL</entry><entry>227</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>DAQTRALAFESGDVDLIYGNGIIGLDTFAQYTK----DKKYVTAISQPMSTRLLLLNAKE</entry><entry>291</entry></row><row><entry /><entry /><entry>D  T   A ESGDVD+IY    +  D   + T+        V  +S P   + ++ ++ +</entry><entry /></row><row><entry>Sbjct:</entry><entry>228</entry><entry>DENTALAALESGDVDMIYATPELA-DKKVKGTRLLDIPSNDVRGLSLPYVKKGVITDSPD</entry><entry>286</entry></row><row><entry /></row><row><entry>Query:</entry><entry>292</entry><entry>------SIFQDKKVRQAMNHAIDKVSIAKNTFRGTEKPADTIFSKSTSHSDAKLNPYSYN</entry><entry>345</entry></row><row><entry /><entry /><entry>       +  D  +R+A+   +++  +      G  KPA +I  K T   + K</entry><entry /></row><row><entry>Sbjct:</entry><entry>287</entry><entry>GYPVGNDVTSDPAIRKALTIGLNRQKVLDTVLNGYGKPAYSIIDK-TPFWNPKTAIKDNK</entry><entry>345</entry></row><row><entry /></row><row><entry>Query:</entry><entry>346</entry><entry>VDKANQLLDQAGWKMGKDKVREKDGKTLTLRLPYIATKATDKDLVTYFQGEWRKIGINVS</entry><entry>405</entry></row><row><entry /><entry /><entry>V KA QLL +AGWK   D  R+K        L Y        +L      + + +GI +</entry><entry /></row><row><entry>Sbjct:</entry><entry>346</entry><entry>VAKAKQLLTKAGWKEQADGSRKKGDLDAAFDLYYPTNDQLRANLAVEVAEQAKALGITIK</entry><entry>405</entry></row><row><entry /></row><row><entry>Query:</entry><entry>406</entry><entry>LIAMEEDDYWANAKKGNFDMMLTYSWGAPWDPHAWMSALTAKADHGHPENIALENLATKT</entry><entry>465</entry></row><row><entry /><entry /><entry>L A      W      + D  L Y+ G       + S   + A  G   NI   N  T T</entry><entry /></row><row><entry>Sbjct:</entry><entry>406</entry><entry>LKASN----WDEMATKSHDSALLYAGGRHHAQQFYESHHPSLAGKGW-TNITFYNNPTVT</entry><entry>460</entry></row><row><entry /></row><row><entry>Query:</entry><entry>466</entry><entry>E-MDRLIKSALVDPKEE</entry><entry>481</entry></row><row><entry /><entry /><entry>+ +D+ + S+ +D   E</entry><entry /></row><row><entry>Sbjct:</entry><entry>461</entry><entry>KYLDKADMTSSDLDKANE</entry><entry>477</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8469&gt; and protein &lt;SEQ ID 8470&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00072" num="00072"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="357pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: 22 Crend: 5</entry><entry /></row><row><entry>McG: Discrim Score: 7.69</entry></row><row><entry>GvH: Signal Score (−7.5): −3.34</entry></row><row><entry>     Possible site: 25</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry>ALOM program count: 0 value: 7.21 threshold: 0.0</entry></row><row><entry>   PERIPHERAL Likelihood = 7.21 273</entry></row><row><entry>modified ALOM score: −1.94</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00006" num="00006"><img id="EMI-C00006" he="203.45mm" wi="119.13mm" file="US07939087-20110510-C00006.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00006" attachment-type="cdx" file="US07939087-20110510-C00006.CDX" /><attachment idref="CHEM-US-00006" attachment-type="mol" file="US07939087-20110510-C00006.MOL" /></attachments></chemistry>

There is also homology to SEQ ID 318. An alignment of the GAS and GBS sequences follows:

<tables id="TABLE-US-00073" num="00073"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 44/186 (23%), Positives = 78/186 (41%), Gaps = 27/186 (14%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>65</entry><entry>VITQMV-DGLLENDEYGNLVPSLAKDWKVSKDGLTYTYTLRDGVSWYTADGEEYAPVTAE</entry><entry>123</entry><entry /></row><row><entry /><entry /><entry>VI  MV +GL+   + G + P+LAK W +S+DG TYT+ LR+      +DG  +    +</entry></row><row><entry>Sbjct:</entry><entry>57</entry><entry>VIQDMVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA---KYSDGSNFNAANVK</entry><entry>113</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>DFVTGLKHAVDDKSDALYVVEDSIKNLKAYQNGEVDFKEVGVKALDDKTVQYTLNKPESY</entry><entry>183</entry></row><row><entry /><entry /><entry>     +    +  +   + + + ++N               +AL+  T +  L   ++Y</entry></row><row><entry>Sbjct:</entry><entry>114</entry><entry>RNFDSIFSKSNRGNHNWFNLTNQLEN---------------YRALNQSTFEIKLK--QAY</entry><entry>156</entry></row><row><entry /></row><row><entry>Query:</entry><entry>184</entry><entry>WNSKTTYSVLFPVNAKFLKS----KGKDFGTTDPSSILVNGAYFLSAFTSKSSMEFHKNE</entry><entry>239</entry></row><row><entry /><entry /><entry>  S T Y +      +FL      KG D    +    +  G + + +      + F +NE</entry></row><row><entry>Sbjct:</entry><entry>157</entry><entry>--SATLYDLSMIRPIRFLSDSAFPKGDDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNE</entry><entry>214</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>NYWDAK</entry><entry>245</entry></row><row><entry /><entry /><entry>NYW  K</entry></row><row><entry>Sbjct:</entry><entry>215</entry><entry>NYWGKK</entry><entry>220</entry></row></tbody></tgroup></table></tables>

SEQ ID 8470 (GBS186) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 35</figref> (lane 7; MW 60 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 41</figref> (lane 6; MW 85.7 kDa).

GBS186-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 202</figref>, lane 4.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 22

A DNA sequence (GBSx0019) was identified in <i>S. agalactiae </i>&lt;SEQ ID 61&gt; which encodes the amino acid sequence &lt;SEQ ID 62&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00074" num="00074"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.95</entry><entry>Transmembrane</entry><entry>101-117 (99-123)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.73</entry><entry>Transmembrane</entry><entry>276-292 (275-293)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.12</entry><entry>Transmembrane</entry><entry>232-248 (232-248)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.96</entry><entry>Transmembrane</entry><entry>151-167 (150-169)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3378(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00075" num="00075"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB04287 GB: AP001509 nickel transport system (permease)</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 119/304 (39%), Positives = 174/304 (57%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>SSIIKKILSAFLALFFISLLTFILIKLSTVNSAENYLRLSKISVSPEALKEAEHYLGLDK</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>S I K+I +    + F   + F+ I+LS V+ AE YL  + I  + E L E  H  GLD+</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>SYIAKRIFAVIPIVLFAIFIMFVFIRLSPVDPAEAYLTAANIHPTEELLAEKRHEFGLDQ</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>PLWKQYWLWFQKALTGDFGYSYVLRLPVLDLVLQRFLATLFLGTSAFLLIVTISTPLGVW</entry><entry>124</entry></row><row><entry /><entry /><entry>P+  QY     K    DFG+SYV   PV D V  R  ATL L  S+  L V IS PLG</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>PMAVQYVQTIVKVFQLDFGHSYVTNQPVWDEVTARMPATLQLAVSSIFLAVLISIPLGFL</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>AGLHESARSDHLIRFLSFSSVSMPNFWVAYLLMLLFSAKLNLLPVSGGNDLQSLILPSIT</entry><entry>184</entry></row><row><entry /><entry /><entry>+ +++++  D   R LS+   S+P FW+ YLL+  FS KLNL PV G      L+LP++T</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>SAIYKNSLIDRFSRLLSYLGASIPQFWLGYLLIFFFSVKLNLFPVEGRGSWAHLVLPTVT</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>LSFSTVGQYIALIRKAISQENRSLNVENARLRGVKERYIVTHHLLRNALPAIMTALSLTW</entry><entry>244</entry></row><row><entry /><entry /><entry>LS + +  Y  L+R ++ ++ +   V  AR RG+KE+ I+  H+L+ A+  ++T L +</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>LSLALIAIYTRLLRASVLEQMQESYVLYARTRGIKEKVIMVKHVLKLAISPVITGLGMNV</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>VYLLTGSIIVEEIFSWNGIGRLFVTSLRTSDLPVIQACMLIFGTLFLANNFMTQCFMNWV</entry><entry>304</entry></row><row><entry /><entry /><entry>  LLTG+IIVE++FSW G GR FV ++   D+PVIQ  +L+   LF+  N +       +</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>GKLLTGTIIVEQVFSWPGFGRYFVDAIFNRDIPVIQCYVLLAACLFIVCNLIVDLVQLAM</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>DPRL</entry><entry>308</entry></row><row><entry /><entry /><entry>DPR+</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>DPRI</entry><entry>306</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 63&gt; which encodes the amino acid sequence &lt;SEQ ID 64&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00076" num="00076"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.27</entry><entry>Transmembrane</entry><entry>290-306 (287-313)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.37</entry><entry>Transmembrane</entry><entry>  12-28 (4-33)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.89</entry><entry>Transmembrane</entry><entry>105-121 (100-128)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.26</entry><entry>Transmembrane</entry><entry>145-161 (142-172)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.39</entry><entry>Transmembrane</entry><entry>191-207 (190-208)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3909(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00077" num="00077"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 102/324 (31%), Positives = 167/324 (51%), Gaps = 28/324 (8%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>IIKKILSAFLALFFISLLTFILIKLSTVN---SAENYLRLSKISVSPEALKEAEHYLGLD</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>II KI+     +F +S+LTF+L+K S V+   ++ NY      S++P   K   H+ GLD</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>IIWKIIRCVTLIFGVSVLTFVLLKQSPVDPVMASVNY----DTSLTPAQYKAIAHHYGLD</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>KPLWKQYWLWFQKALTGDFGYSYVLRLPVLDLVLQRFLATLFLGTSAFLLIVTISTPLGV</entry><entry>123</entry></row><row><entry /><entry /><entry>KP   QY++W +  + GD G S V R PV D++  R  A+  L   +++L   I   LG</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>KPALVQYFIWLKNVIQGDLGTSLVYRQPVSDIIRSRAGASFILMGLSWILSGLIGFILGT</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>WAGLHESARSDHLIRFLSFSSVSMPNFWVAYLLMLLFSAKLNLLPVSGGNDL--------</entry><entry>175</entry></row><row><entry /><entry /><entry> +  H+    D ++R+ S+  +S+P FW+  + +L+FS +L   P+   + +</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>LSAFHQGKLLDRVVRWFSYLQISVPTFWIGLIFLLIFSVQLGWFPIGISSPIGTLSQDIT</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>-----QSLILPSITLSFSTVGQYIALIRKAISQENRSLNVENARLRGVKERYIVTHHLLR</entry><entry>230</entry></row><row><entry /><entry /><entry>     + L+LP  TLS   +       R  +     S  V  AR RG  +  I  HH LR</entry></row><row><entry>Sbjct:</entry><entry>184</entry><entry>LADRVKHLMLPVFTLSILGIANVTLHTRTKMMSVLSSEYVLFARARGETQWQIFKHHCLR</entry><entry>243</entry></row><row><entry /></row><row><entry>Query:</entry><entry>231</entry><entry>NALPAIMTALSLTWVY---LLTGSIIVEEIFSWNGIGRLFVTSLRTSDLPVIQACMLIFG</entry><entry>287</entry></row><row><entry /><entry /><entry>N   AI+ A++L + Y   L  GS++ E++FS+ G+G     +   SD P++ A ++I G</entry></row><row><entry>Sbjct:</entry><entry>244</entry><entry>N---AIVPAITLHFSYFGELFGGSVLAEQVFSYPGLGSTLTEAGLKSDTPLLLAIVMI-G</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>288</entry><entry>TLFL-ANNFMTQCFMNWVDPRLRK</entry><entry>310</entry></row><row><entry /><entry /><entry>TLF+ A N +     + ++P+LR+</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>TLFVFAGNLIADILNSIINPQLRR</entry><entry>323</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 23

A DNA sequence (GBSx0020) was identified in <i>S. agalactiae </i>&lt;SEQ ID 65&gt; which encodes the amino acid sequence &lt;SEQ ID 66&gt;. This protein is predicted to be nickel transport system (permease). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00078" num="00078"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.64</entry><entry>Transmembrane</entry><entry>  57-73 (51-80)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.85</entry><entry>Transmembrane</entry><entry>173-189 (169-194)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry> 94-110 (86-112)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.44</entry><entry>Transmembrane</entry><entry>221-237 (221-238)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>118-134 (118-134)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4057(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00079" num="00079"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB04288 GB: AP001509 nickel transport system (permease)</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 103/239 (43%), Positives = 157/239 (65%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>AIFAPILSSFDPQYVDLSQKLLAPNNVHLLGTDQLGRDVLSRLLYGARYSLFLAIIISLL</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>AI AP ++  DP  V+L+ KLL P+  + LGTDQLGR  LSRLL+GAR SL  A +I +</entry></row><row><entry>Sbjct:</entry><entry>29</entry><entry>AILAPWIAPHDPIQVNLALKLLPPSWEYPLGTDQLGRCNLSRLLFGARVSLGFATLIFIS</entry><entry>88</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>ELTIGMFVGLIVGWYQGKLENLFLWIANIILAFPSFLLSLATVGILGHGLGNLIFAIVFV</entry><entry>125</entry></row><row><entry /><entry /><entry> L IG+ VG I G+  G ++++ +     ++AFP+ +L L  VG+ G GL  ++ A+V V</entry></row><row><entry>Sbjct:</entry><entry>89</entry><entry>SLGIGLLVGAIAGYRGGWIDSVLMRFCEGVMAFPNLVLVLGLVGLFGPGLWQVVLALVMV</entry><entry>148</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>EWVYYAKLMTNLVKSAKKEPYVINAQIMGLSVWHILRKHIFPFVYQPILVMVLMNIGNII</entry><entry>185</entry></row><row><entry /><entry /><entry>+WVYYA++  +++ S K++ ++  A+I G S W I+R+HI P V  PI+V+  + +G  I</entry></row><row><entry>Sbjct:</entry><entry>149</entry><entry>QWVYYARMFRSMIVSLKEQNFITAARISGSSPWKIIRRHIIPNVLPPIVVIGTLEMGWAI</entry><entry>208</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>LMISGFSFLGIGVQPNVTEWGMMLHDARGYFRTATWMMLSPGIAIFLTVFSFNTLGDAI</entry><entry>244</entry></row><row><entry /><entry /><entry>+ IS  SFLG+G+QP   EWG M+H+ + + R+   +ML PGI I L V +FN LG+++</entry></row><row><entry>Sbjct:</entry><entry>209</entry><entry>MDISALSFLGLGIQPPTPEWGAMIHEGKSFIRSHPELMLYPGIMILLVVMTFNVLGESL</entry><entry>267</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 67&gt; which encodes the amino acid sequence &lt;SEQ ID 68&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00080" num="00080"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.80</entry><entry>Transmembrane</entry><entry>182-198 (180-204)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.38</entry><entry>Transmembrane</entry><entry>  77-93 (69-98)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.06</entry><entry>Transmembrane</entry><entry>112-128 (104-132)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.16</entry><entry>Transmembrane</entry><entry>   8-24 (7-31)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.10</entry><entry>Transmembrane</entry><entry>239-255 (235-258)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4121(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00081" num="00081"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 61/246 (24%), Positives = 127/246 (50%), Gaps = 1/246 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>LVISAIFAPILSSFDPQYVDLSQKLLAPNNVHLLGTDQLGRDVLSRLLYGARYSLFLAII</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>L++S +   +     P   + + + LAP+  HL GTD LGRD+  R + G  +SL + ++</entry></row><row><entry>Sbjct:</entry><entry>19</entry><entry>LILSILALNLYFYRTPLETNAALRNLAPSLNHLFGTDGLGRDMFVRTIRGLYFSLQVGLL</entry><entry>78</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>ISLLELTIGMFVGLIVGWYQGKLENLFLWIANIILAFPSFLLSLATVGILGHGLGNLIFA</entry><entry>121</entry></row><row><entry /><entry /><entry> +L+ + +    G++ G     ++ +  W+ ++ +  P  +  +    ++G G   +I A</entry></row><row><entry>Sbjct:</entry><entry>79</entry><entry>GALMGVFLATVFGVLAGLGNSLIDKIIAWLVDLFIGMPHLIFMILISFVVGKGAQGVIIA</entry><entry>138</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>IVFVEWVYYAKLMTNLVKSAKREPYVINAQIMGLSVWHILRKHIFPFVYQPILVMVLMNI</entry><entry>181</entry></row><row><entry /><entry /><entry>     W   A+L+ N V   K + +V  ++ MG + ++I+R HI P +   I +  ++</entry></row><row><entry>Sbjct:</entry><entry>139</entry><entry>TAVTHWPSLARLIRNEVYDLKNKAFVQLSKSMGKTPYYIVRHHILPLIASQIFIGFILLF</entry><entry>198</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>GNIILMISGFSFLGIGVQPNVTEWGMMLHDARGYFRTAT-WMMLSPGIAIFLTVFSFNTL</entry><entry>240</entry></row><row><entry /><entry /><entry> ++IL  +  +FLG G+       G++L +A  +      W+++ PG+ + L V +F+T+</entry></row><row><entry>Sbjct:</entry><entry>199</entry><entry>PHVILHEASMTFLGFGLSAEQPSVGIILSEAAKHISLGNWWLVIFPGLYLILVVNAFDTI</entry><entry>258</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDAIDK</entry><entry>246</entry></row><row><entry /><entry /><entry>G+++ K</entry></row><row><entry>Sbjct:</entry><entry>259</entry><entry>GESLKK</entry><entry>264</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8473&gt; and protein &lt;SEQ ID 8474&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00082" num="00082"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 0</entry><entry /></row><row><entry>McG: Discrim Score: 7.56</entry></row><row><entry>GvH: Signal Score (−7.5): −1.15</entry></row><row><entry>     Possible site: 14</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry>ALOM program count: 5 value: −7.64 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.64</entry><entry>Transmembrane</entry><entry>  57-73 (51-80)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.85</entry><entry>Transmembrane</entry><entry>173-189 (169-194)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry> 94-110 (86-112)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.44</entry><entry>Transmembrane</entry><entry>221-237 (221-238)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>118-134 (118-134)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 4.72</entry><entry>145</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.03</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.4057(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00007" num="00007"><img id="EMI-C00007" he="107.27mm" wi="119.21mm" file="US07939087-20110510-C00007.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00007" attachment-type="cdx" file="US07939087-20110510-C00007.CDX" /><attachment idref="CHEM-US-00007" attachment-type="mol" file="US07939087-20110510-C00007.MOL" /></attachments></chemistry>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 24

A DNA sequence (GBSx0021) was identified in <i>S. agalactiae </i>&lt;SEQ ID 69&gt; which encodes the amino acid sequence &lt;SEQ ID 70&gt;. This protein is predicted to be peptide ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00083" num="00083"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 60</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.32</entry><entry>Transmembrane</entry><entry>161-177 (161-177)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1128(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10027&gt; which encodes amino acid sequence &lt;SEQ ID 10028&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00084" num="00084"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF73561 GB: AE002315 peptide ABC transporter, ATP-binding</entry><entry /></row><row><entry>protein [<i>Chlamydia muridarum</i>]</entry></row><row><entry>Identities = 86/253 (33%), Positives = 154/253 (59%), Gaps = 2/253 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>METTMEQLEIRKLSLQIGEVPVLRDFSCKIDMGESLTIIGESGSGKTLLAKLLVGHIPQG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  T+ ++E   ++++     ++   S  I   +SL ++GE+GSGKT ++K ++G +P</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKTLLKIENLVVAIKESNQRLVNHLSLTIKQRQSLALVGENGSGKTTVSKAILGFLPDN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>MTVR-GNIFFKGVDLGKLTVKQWQKLRGRDIAYLVQNPMSMFNPFQKIEAHILETILSHE</entry><entry>119</entry></row><row><entry /><entry /><entry>  ++ G IF+ G D+ +L+ K++Q +RG+ I+ + QN M    P  ++   I+ET+  H</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>CCIQSGKIFYSGTDITRLSRKEFQSIRGKKISTIFQNAMGTLTPSMRVGTQIIETLRHHF</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>KCSKRVALSKALEWMKRLNLDDAISLLKKYPFELSGGMLQRIMLATILSLDPQVIILDEP</entry><entry>179</entry></row><row><entry /><entry /><entry>  SK  A +KA E +  ++++     L+ YPFELSGGM QR+ +A  L+ +P++II DEP</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VMSKEEAFAKARELLVSVHIESPDRCLQLYPFELSGGMCQRVSIAIALATNPELIIADEP</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>TSAVDCHNCSTISAILQEL-QNNGKTLITVTHDYQLARDLGGQLLVISEGEVVEQGQTQA</entry><entry>238</entry></row><row><entry /><entry /><entry>++A+D  + + +  +L+++ QNN   L+ +TH+  L  +L  ++ +I  GE+VEQG</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>STALDSISQAQVLRVLKQIHQNNNTALLLITHNLALVSELCEEMAIIHHGEIVEQGPVHE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>239</entry><entry>ILSNPQHNYTKAL</entry><entry>251</entry></row><row><entry /><entry /><entry>+L +P H YT+ L</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LLRSPSHPYTQKL</entry><entry>253</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 71&gt; which encodes the amino acid sequence &lt;SEQ ID 72&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00085" num="00085"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.50</entry><entry>Transmembrane</entry><entry>168-184 (167-184)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.70</entry><entry>Transmembrane</entry><entry>211-227 (211-227)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1999(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00086" num="00086"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 87/232 (37%), Positives = 138/232 (58%), Gaps = 3/232 (1%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>23</entry><entry>LRDFSCKIDMGESLTIIGESGSGKTLLAKLLVGHIPQ-GMTVRGNIFFKGVDLGKL-TVK</entry><entry>80</entry><entry /></row><row><entry /><entry /><entry>+R+ S ++  GE L  +GESGSGK++L K   G +   G    G+I ++G +L  L T K</entry></row><row><entry>Sbjct:</entry><entry>28</entry><entry>IRNVSLELVEGEVLAFVGESGSGKSVLTKTFTGMLESNGRIANGSIVYRGQELTDLKTNK</entry><entry>87</entry></row><row><entry /></row><row><entry>Query:</entry><entry>81</entry><entry>QWQKLRGRDIAYLVQNPMSMFNPFQKIEAHILETILSHEKCSKRVALSKALEWMKRLNLD</entry><entry>140</entry></row><row><entry /><entry /><entry>+W K+RG  IA + Q+PM+  +P + I + I E I+ H+K S   A   AL++M ++ +</entry></row><row><entry>Sbjct:</entry><entry>88</entry><entry>EWAKIRGSKIATIFQDPMTSLSPIKTIGSQITEVIIKHQKVSHAKAKEMALDYMNKVGIP</entry><entry>147</entry></row><row><entry /></row><row><entry>Query:</entry><entry>141</entry><entry>DAISLLKKYPFELSGGMLQRIMLATILSLDPQVIILDEPTSAVDCHNCSTISAILQELQN</entry><entry>200</entry></row><row><entry /><entry /><entry>+A     + YPFE SGGM QRI++A  L+  P ++I DEPT+A+D    + I  +L+ LQ</entry></row><row><entry>Sbjct:</entry><entry>148</entry><entry>NAKKRFEDYPFEYSGGMRQRIVIAIALACRPDILICDEPTTALDVTIQAQIVELLKSLQR</entry><entry>207</entry></row><row><entry /></row><row><entry>Query:</entry><entry>201</entry><entry>NGK-TLITVTHDYQLARDLGGQLLVISEGEVVEQGQTQAILSNPQHNYTKAL</entry><entry>251</entry></row><row><entry /><entry /><entry>    T+I +THD  +   +  ++ V+  GE+VE G  + I  +P+H YT +L</entry></row><row><entry>Sbjct:</entry><entry>208</entry><entry>EYHFTIIFITHDLGVVASIADKVAVMYAGEIVEFGTVEEIFYDPRHPYTWSL</entry><entry>259</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 25

A DNA sequence (GBSx0022) was identified in <i>S. agalactiae </i>&lt;SEQ ID 73&gt; which encodes the amino acid sequence &lt;SEQ ID 74&gt;. This protein is predicted to be peptide ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00087" num="00087"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10025&gt; which encodes amino acid sequence &lt;SEQ ID 10026&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00088" num="00088"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05797 GB: AP001514 oligopeptide ABC transporter (ATP-binding</entry><entry /></row><row><entry>protein) [<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 82/199 (41%), Positives = 130/199 (65%), Gaps = 2/199 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>19</entry><entry>RQEVLKDCHFHLKRGEIIGIMGKSGSGKSSLARLIIGLIDSPTCGSIYFQG-KIYTPKDGK</entry><entry>77</entry><entry /></row><row><entry /><entry /><entry>+Q++L    F  + GE +GI+G+SGSGKS+L RL++G++ P  G IYF+G K+</entry></row><row><entry>Sbjct:</entry><entry>21</entry><entry>KQKILNHISFECRHGECLGIIGESGSGKSTLGRLLLGIEKPDRGHIYFEGNKVEERSVRS</entry><entry>80</entry></row><row><entry /></row><row><entry>Query:</entry><entry>78</entry><entry>AQIILVFQDALSSVNPYFSIEEILNEAFYGKKTT-FELCQILEAVGLDGTYLKYKARQLS</entry><entry>136</entry></row><row><entry /><entry /><entry>  I  VFQD  SS+NP+F++E  + E   GKK    ++  +L+ VGL  +Y K    +LS</entry></row><row><entry>Sbjct:</entry><entry>81</entry><entry>GNISAVFQDYTSSINPFFTVETAIMEPLKGKKAAKSKVDYLLKQVGLHPSYKKKYPHELS</entry><entry>140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>GGQLQRVCIARALLLKPKIIIFDESLSGLDPVTQIKMLRLLQKIKRRYELSFIMISHDPK</entry><entry>196</entry></row><row><entry /><entry /><entry>GG++QRVCIARA+  +PK I+ DE++S LD   Q ++L LL ++KR Y++S++ I+HD +</entry></row><row><entry>Sbjct:</entry><entry>141</entry><entry>GGEVQRVCIARAISTEPKCIVLDEAISSLDVSIQTQVLDLLIELKRIYQMSYLFITHDIQ</entry><entry>200</entry></row><row><entry /></row><row><entry>Query:</entry><entry>197</entry><entry>ICQAICNRVFLIKNGYLVE</entry><entry>215</entry></row><row><entry /><entry /><entry>    IC+R+ + ++G + E</entry></row><row><entry>Sbjct:</entry><entry>201</entry><entry>AAAYICDRIMIFRHGQIEE</entry><entry>219</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 75&gt; which encodes the amino acid sequence &lt;SEQ ID 76&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00089" num="00089"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 60</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3195(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00090" num="00090"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 91/238 (38%), Positives = 137/238 (57%), Gaps = 21/238 (8%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKEIFLMLVCNHVGKTFGRQ----EVLKDCHFHLKRGEIIGIMGKSGSGKSSLARLIIGL</entry><entry>56</entry><entry /></row><row><entry /><entry /><entry>M E  + L  +H+  TF ++    E +KD   H+ +G+I GI+G SG+GKS+L R+I  L</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNEAIIQL--DHIDITFRQKKRVIEAVKDVTVHINQGDIYGIVGYSGAGKSTLVRVINLL</entry><entry>58</entry></row><row><entry /></row><row><entry>Query:</entry><entry>57</entry><entry>DSPTCGSI-------YFQGKIYTPKDGKAQ----IILVFQ--DALSSVNPYFSIEEILNE</entry><entry>103</entry></row><row><entry /><entry /><entry> +PT G I       + QGKI    D   Q    I ++FQ  + ++      ++   L</entry></row><row><entry>Sbjct:</entry><entry>59</entry><entry>QAPTNGKITVDGDVTFDQGKIQLSADALRQKRRDIGMIFQHFNLMAQKTAKENVAFALRH</entry><entry>118</entry></row><row><entry /></row><row><entry>Query:</entry><entry>104</entry><entry>AFYGK-KTTFELCQILEAVGLDGTYLKYKARQLSGGQLQRVCIARALLLKPKIIIFDESL</entry><entry>162</entry></row><row><entry /><entry /><entry>+   K +   ++ ++LE VGL      Y A QLSGGQ QRV IARAL   PKI+I DE+</entry></row><row><entry>Sbjct:</entry><entry>119</entry><entry>SSLSKTEKEHKVIELLELVGLSERADNYPA-QLSGGQKQRVAIARALANDPKILISDEAT</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>163</entry><entry>SGLDPVTQIKMLRLLQKIKRRYELSFIMISHDPKICQAICNRVFLIKNGYLVEDNEFL</entry><entry>220</entry></row><row><entry /><entry /><entry>S LDP T  ++L LLQ++ R+  L+ +MI+H+ +I + ICNRV +++NG L+E+   L</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>SALDPKTTKQILALLQELNRKLGLTIVMITHEMQIVKDICNRVAVMQNGVLIEEGSVL</entry><entry>235</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 26

A DNA sequence (GBSx0023) was identified in <i>S. agalactiae </i>&lt;SEQ ID 77&gt; which encodes the amino acid sequence &lt;SEQ ID 78&gt;. This protein is predicted to be UMP kinase (pyrH). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00091" num="00091"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1935(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00092" num="00092"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB13524 GB: Z99112 uridylate kinase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 143/238 (60%), Positives = 193/238 (81%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>EPKYQRILIKLSGEALAGDKGVGIDIPTVQSIAKEIAEVHNSGVQIALVIGGGNLWRGEP</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+PKY+RI++KLSGEALAG++G GI+   +QSIAK++ E+    V++A+V+GGGN    +</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>KPKYKRIVLKLSGEALAGEQGNGINPTVIQSIAKQVKEIAELEVEVAVVVGGGNYGAEKT</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>AAEAGMDRVQADYTGMLGTVMNALVMADSLQQYGVDTRVQTAIPMQTVAEPYVRGRALRH</entry><entry>121</entry></row><row><entry /><entry /><entry> ++ GMDR  ADY GML TVMN+L + DSL+  G+ +RVQT+I M+ VAEPY+R +A+RH</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>GSDLGMDRATADYMGMLATVMNSLALQDSLETLGIQSRVQTSIEMRQVAEPYIRRKAIRH</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>LEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEAEAILMAKNGVDGVYNADPKKDANAVKF</entry><entry>181</entry></row><row><entry /><entry /><entry>LEK R+V+F AG G+PYFSTDTTAALRAAEIEA+ ILMAKN VDGVYNADP+KD +AVK+</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>LEKKRVVIFAAGTGNPYFSTDTTAALRAAEIEADVILMAKNNVDGVYNADPRKDESAVKY</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>DELTHVEVIKRGLKIMDATASTISMDNDIDLVVFNMNETGNIKRVVLGEQIGTTVSNK</entry><entry>239</entry></row><row><entry /><entry /><entry>+ L++++V+K GL++MD+TAS++ MDNDI L+VF++ E GNIKR V+GE IGT V  K</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>ESLSYLDVLKDGLEVMDSTASSLCMDNDIPLIVFSIMEEGNIKRAVIGESIGTIVRGK</entry><entry>240</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 79&gt; which encodes the amino acid sequence &lt;SEQ ID 80&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00093" num="00093"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1955(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00094" num="00094"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 224/242 (92%), Positives = 233/242 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEPKYQRILIKLSGEALAGDKGVGIDIPTVQSIAKEIAEVHNSGVQIALVIGGGNLWRGE</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+EPKYQRILIKLSGEALAG+KGVGIDIPTVQ+IAKEIAEVH SGVQIALVIGGGNLWRGE</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>VEPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>PAAEAGMDRVQADYTGMLGTVMNALVMADSLQQYGVDTRVQTAIPMQTVAEPYVRGRALR</entry><entry>120</entry></row><row><entry /><entry /><entry>PAA+AGMDRVQADYTGMLGTVMNALVMADSLQ YGVDTRVQTAIPMQ VAEPY+RGRALR</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PAADAGMDRVQADYTGMLGTVMNALVMADSLQHYGVDTRVQTAIPMQNVAEPYIRGRALR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEAEAILMAKNGVDGVYNADPKKDANAVK</entry><entry>180</entry></row><row><entry /><entry /><entry>HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEA+AILMAKNGVDGVYNADPKKDANAVK</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILMAKNGVDGVYNADPKKDANAVK</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>FDELTHVEVIKRGLKIMDATASTISMDNDIDLVVFNMNETGNIKRVVLGEQIGTTVSNKA</entry><entry>240</entry></row><row><entry /><entry /><entry>FDELTH EVIKRGLKIMDATAST+SMDNDIDLVVFNMNE GNI+RVV GE IGTTVSNK</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>FDELTHGEVIKRGLKIMDATASTLSMDNDIDLVVFNMNEAGNIQRVVFGEHIGTTVSNKV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>SE</entry><entry>242</entry></row><row><entry /><entry /><entry> +</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>CD</entry><entry>242</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 27

A DNA sequence (GBSx0024) was identified in <i>S. agalactiae </i>&lt;SEQ ID 81&gt; which encodes the amino acid sequence &lt;SEQ ID 82&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00095" num="00095"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3712(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 28

A DNA sequence (GBSx0025) was identified in <i>S. agalactiae </i>&lt;SEQ ID 83&gt; which encodes the amino acid sequence &lt;SEQ ID 84&gt;. This protein is predicted to be ribosome recycling factor (frr). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00096" num="00096"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 34</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3522(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00097" num="00097"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06143 GB: AP001515 ribosome recycling factor [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 112/185 (60%), Positives = 149/185 (80%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="center" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTKEIVTKAQERFEQSHQSLSREFAGIRAGRANASLLDRIQVEYYGAPTPLNQLASITVP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+KE++  A++R  ++ ++L RE A +RAGRAN ++LDRI VEYYGA TPLNQLA+I+VP</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKEVLNDAEQRMTKATEALGRELAKLRAGRANPAMLDRITVEYYGAETPLNQLATISVP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EARVLLISPFDKSSIKDIERAINESDLGINPANDGSVIRLVIPALTEETRRDLAKEVKKV</entry><entry>120</entry></row><row><entry /><entry /><entry>EAR+L+I PFDKSSI DIERAI +SDLG+ P+NDG+VIR+ IP LTEE RRDL K VKK</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>EARLLVIQPFDKSSISDIERAIQKSDLGLTPSNDGTVIRITIPPLTEERRRDLTKLVKKS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GENAKIAIRNIRRDAMDEAKKQEKNKEITEDDLKSLEKDIQKATDDAVKHIDEMTANKEK</entry><entry>180</entry></row><row><entry /><entry /><entry> E AK+A+RNIRRDA D+ KK++K+ E+TEDDL+ + +D+QK TD  ++ ID+    KEK</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>AEEAKVAVRNIRRDANDDLKKRQKDGELTEDDLRRVTEDVQKLTDKYIEQIDQKAEAKEK</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>ELLEV</entry><entry>185</entry></row><row><entry /><entry /><entry>E++EV</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>EIMEV</entry><entry>185</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 85&gt; which encodes the amino acid sequence &lt;SEQ ID 86&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00098" num="00098"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4462(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00099" num="00099"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 160/185 (86%), Positives = 171/185 (91%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTKEIVTKAQERFEQSHQSLSREFAGIRAGRANASLLDRIQVEYYGAPTPLNQLASITVP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M   I+  A+ERF QSHQSLSRE+A IRAGRANASLLDRIQV+YYGAPTPLNQLASITVP</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MANAIIETAKERFAQSHQSLSREYASIRAGRANASLLDRIQVDYYGAPTPLNQLASITVP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EARVLLISPFDKSSIKDIERAINESDLGINPANDGSVIRLVIPALTEETRRDLAKEVKKV</entry><entry>120</entry></row><row><entry /><entry /><entry>EARVLLISPFDKSSIRDIERA+N SDLGI PANDGSVIRLVIPALTEETR++LAKEVKKV</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>EARVLLISPFDKSSIKDIERALNASDLGITPANDGSVIRLVIPALTEETRKELAKEVKKV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GENAKIAIRNIRRDAMDEAKKQEKNKEITEDDLKSLEKDIQKATDDAVKHIDEMTANKEK</entry><entry>180</entry></row><row><entry /><entry /><entry>GENAKIAIRNIRRDAMD+AKKQEK KEITED+LK+LEKDIQKATDDA+K ID MTA KEK</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GENAKIAIRNIRRDAMDDAKKQEKAKEITEDELKTLEKDIQKATDDAIKEIDRMTAEKEK</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>ELLEV</entry><entry>185</entry></row><row><entry /><entry /><entry>ELL V</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>ELLSV</entry><entry>185</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 29

A DNA sequence (GBSx0026) was identified in <i>S. agalactiae </i>&lt;SEQ ID 87&gt; which encodes the amino acid sequence &lt;SEQ ID 88&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00100" num="00100"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1356(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10023&gt; which encodes amino acid sequence &lt;SEQ ID 10024&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00101" num="00101"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB12943 GB: Z99109 yitL [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 107/269 (39%), Positives = 155/269 (56%), Gaps = 6/269 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>42</entry><entry>LVTDENKDF-YFIQKDGFTFALSKSEGEHHIGEM--VKGFAYTDMQQKARLTTKETFATR</entry><entry>98</entry><entry /></row><row><entry /><entry /><entry>L  D   DF YF+     T  L  SE    I +   V+ F Y D Q++   T K    +</entry></row><row><entry>Sbjct:</entry><entry>25</entry><entry>LSIDHQTDFGYFLTDGEDTILLHNSEMTEDIEDRDEVEVFIYVDQQERLAATMKIPIISA</entry><entry>84</entry></row><row><entry /></row><row><entry>Query:</entry><entry>99</entry><entry>DHYGWGTVTEVRKDLGVFLDTGLPDKQVVVSLDVLPELKELWPKKGDRLYVCLDVDKKDR</entry><entry>158</entry></row><row><entry /><entry /><entry>D YGW  V +  +D+GVF+D GL  K  +V+ + LP  +++WP+KGD+LY  L V  + R</entry></row><row><entry>Sbjct:</entry><entry>85</entry><entry>DEYGWVEVVDKVEDMGVFVDVGL-SKDALVATEHLPPYEDVWPQKGDKLYCMLKVTNRGR</entry><entry>143</entry></row><row><entry /></row><row><entry>Query:</entry><entry>159</entry><entry>LWALPADPEVFQRMATPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYSE</entry><entry>218</entry></row><row><entry /><entry /><entry>++A PA  ++   + T A  ++ N+     VYRL  SG+FV + ++ +  FIHPSER  E</entry></row><row><entry>Sbjct:</entry><entry>144</entry><entry>MFAKPAPEDIISELFTDASEDLMNKELTGTVYRLIASGSFV-ITDDGIRCFIHPSERKEE</entry><entry>202</entry></row><row><entry /></row><row><entry>Query:</entry><entry>219</entry><entry>PRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMILTYLESNGGFMTLNDKSSPE</entry><entry>278</entry></row><row><entry /><entry /><entry>PRLG  +  RVI  +E D ++NLSL PR  + +  DA+ ILTY+    G M  +DKS P+</entry></row><row><entry>Sbjct:</entry><entry>203</entry><entry>PRLGSRVTGRVIQVKE-DGSVNLSLLPRKQDAMSVDAECILTYMRMRNGAMPYSDKSQPD</entry><entry>261</entry></row><row><entry /></row><row><entry>Query:</entry><entry>279</entry><entry>EIKATFGISKGQFKKALGGLMKAKKIKQD</entry><entry>307</entry></row><row><entry /><entry /><entry>+I+  F +SK  FK+ALG LMK  K+ Q+</entry></row><row><entry>Sbjct:</entry><entry>262</entry><entry>DIRERFNMSKAAFKRALGHLMKNGKVYQE</entry><entry>290</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 89&gt; which encodes the amino acid sequence &lt;SEQ ID 90&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00102" num="00102"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0811(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00103" num="00103"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 235/284 (82%), Positives = 265/284 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>31</entry><entry>MNTLLATVITGLVTDENKDFYFIQKDGFTFALSKSEGEHHIGEMVKGFAYTDMQQKARLT</entry><entry>90</entry><entry /></row><row><entry /><entry /><entry>MN LLATVITGL+ +EN + YFI K+GFTF LSK+EGE  IG+MV GFAYTD++QKARLT</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNDLLATVITGLIKEENANDYFIHKEGFTFTLSKAEGERQIGDMVTGFAYTDIEQKARLT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>91</entry><entry>TKETFATRDHYGWGTVTEVRKDLGVFLDTGLPDKQVVVSLDVLPELKELWPKKGDRLYVC</entry><entry>150</entry></row><row><entry /><entry /><entry>TKE  +TR  YGWG VTEVR+DLGVF+DTG+P+K++VVSLDVLPE+KELWPKKGD+LY+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TKEIRSTRTSYGWGEVTEVRRDLGVFVDTGIPNKEIVVSLDVLPEMKELWPKKGDKLYIR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>151</entry><entry>LDVDKKDRLWALPADPEVFQRMATPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFI</entry><entry>210</entry></row><row><entry /><entry /><entry>LDVDKKDR+W LPA+PEVFQ+MA+PAYNNMQNQ+WPAIVYRLKL+GTFVYLPENNMLGFI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LDVDKKDRIWGLPAEPEVFQKMASPAYNNMQNQHWPAIVYRLKLTGTFVYLPENNMLGFI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>211</entry><entry>HPSERYSEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMILTYLESNGGFMT</entry><entry>270</entry></row><row><entry /><entry /><entry>H SERY+EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMI+TYLE+NGGFMT</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>HSSERYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMIVTYLEANGGFMT</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>271</entry><entry>LNDKSSPEEIKATFGISKGQFKKALGGLMKAKKIKQDQLGTELL</entry><entry>314</entry></row><row><entry /><entry /><entry>LNDKSSPEEIKA+FGISKGQFKKALGGLMKAK+IKQD  GTEL+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LNDKSSPEEIKASFGISKGQFKKALGGLMKAKRIKQDATGTELI</entry><entry>284</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 30

A DNA sequence (GBSx0028) was identified in <i>S. agalactiae </i>&lt;SEQ ID 91&gt; which encodes the amino acid sequence &lt;SEQ ID 92&gt;. This protein is predicted to be peptide methionine sulfoxide reductase (msrA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00104" num="00104"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 33</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0866(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10021&gt; which encodes amino acid sequence &lt;SEQ ID 10022&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00105" num="00105"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05167 GB: AP001512 peptide methionine sulfoxide reductase</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 102/173 (58%), Positives = 126/173 (71%), Gaps = 2/173 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>14</entry><entry>ENDMERAIFAGGCFWCMVQPFEELDGIESVLSGYTGGHVENPTYKEVCSKTTGHTEAVEI</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>E+    A FAGGCFWCMV PFEE  GI  V+SGYTGGH ENPTYKEVCS+TTGH EAV+I</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>ESKWALATFAGGCFWCMVSPFEEEPGIHQVVSGYTGGHTENPTYKEVCSETTGHYEAVQI</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>IFNPEKISYADLVELYWAQTDPTDAFGQFEDRGDNYRPVIFYENEEQRQIAQKSKDKLQA</entry><entry>133</entry></row><row><entry /><entry /><entry> F+PE   Y  L+E+YW Q DPTD  GQF DRGD+YR  IFY +E+Q+Q A  SK KL+</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>SFDPEVFPYEKLLEIYWTQIDPTDPGGQFHDRGDSYRTAIFYHDEQQKQAADASKQKLEE</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>134</entry><entry>SGRFDRPIVTSIEPADTFYPAEDYHQAFYRTNPARYAL--SSARRHAFLEENW</entry><entry>184</entry></row><row><entry /><entry /><entry>SG+F+ PIVT I PA  FYPAE+YHQ +++ NP  Y +    + R AF++++W</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>SGKFNAPIVTRILPAKPFYPAEEYHQKYHKKNPFHYKMYRHGSGREAFIKQHW</entry><entry>175</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 93&gt; which encodes the amino acid sequence &lt;SEQ ID 94&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00106" num="00106"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0084(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>RGD motif: 89-91</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00107" num="00107"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05167 GB: AP001512 peptide methionine sulfoxide reductase</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 98/168 (58%), Positives = 125/168 (74%), Gaps = 4/168 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>AIFAGGCFWCMVQPFEEQAGILSVRSGYTGGHLPNPSYEQVCAKTTGHTEAVEIIFDPKQ</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>A FAGGCFWCMV PFEE+ GI  V SGYTGGH  NP+Y++VC++TTGH EAV+I FDP+</entry></row><row><entry>Sbjct:</entry><entry>9</entry><entry>ATFAGGCFWCMVSPFEEEPGIHQVVSGYTGGHTENPTYKEVCSETTGHYEAVQISFDPEV</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>IAYKDLVELYWTQTDPTDAFGQFEDRGDNYRPVIYYTTERQKEIAEQSKANLQASGRFDQ</entry><entry>123</entry></row><row><entry /><entry /><entry>  Y+ L+E+YWTQ DPTD  GQF DRGD+YR  I+Y  E+QK+ A+ SK  L+ SG+F+</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>FPYEKLLEIYWTQIDPTDPGGQFHDRGDSYRTAIFYHDEQQKQAADASKQKLEESGKFNA</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>PIVTTIEPAEPFYLAEDYHQGFYKKNP---KRYAQSSAIRHQFLEENW</entry><entry>168</entry></row><row><entry /><entry /><entry>PIVT I PA+PFY AE+YHQ ++KKNP   K Y   S  R  F++++W</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>PIVTRILPAKPFYPAEEYHQKYHKKNPFHYKMYRHGSG-REAFIKQHW</entry><entry>175</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00108" num="00108"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 130/168 (77%), Positives = 148/168 (87%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>MERAIFAGGCFWCMVQPFEELDGIESVLSGYTGGHVENPTYKEVCSKTTGHTEAVEIIFN</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>MERAIFAGGCFWCMVQPFEE  GI SV SGYTGGH+ NP+Y++VC+KTTGHTEAVEIIF+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MERAIFAGGCFWCMVQPFEEQAGILSVRSGYTGGHLPNPSYEQVCAKTTGHTEAVEIIFD</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>77</entry><entry>PEKISYADLVELYWAQTDPTDAFGQFEDRGDNYRPVIFYENEEQRQIAQKSKDKLQASGR</entry><entry>136</entry></row><row><entry /><entry /><entry>P++I+Y DLVELYW QTDPTDAFGQFEDRGDNYRPVI+Y  E Q++IA++SK  LQASGR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PKQIAYKDLVELYWTQTDPTDAFGQFEDRGDNYRPVIYYTTERQKEIAEQSKANLQASGR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>FDRPIVTSIEPADTFYPAEDYHQAFYRTNPARYALSSARRHAFLEENW</entry><entry>184</entry></row><row><entry /><entry /><entry>FD+PIVT+IEPA+ FY AEDYHQ FY+ NP RYA SSA RH FLEENW</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>FDQPIVTTIEPAEPFYLAEDYHQGFYKKNPKRYAQSSAIRHQFLEENW</entry><entry>168</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 31

A DNA sequence (GBSx0029) was identified in <i>S. agalactiae </i>&lt;SEQ ID 95&gt; which encodes the amino acid sequence &lt;SEQ ID 96&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00109" num="00109"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2727(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00110" num="00110"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB13859 GB: Z99114 yozE [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 24/66 (36%), Positives = 42/66 (63%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KSFYSWLMTQRNPKSNEPVAILADYAFDETTFPKHSSDFETVSRYLEDEASFSFNLTDFD</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>KSFY +L+  R+PK  + ++  A+ A+++ +FPK S+D+  +S YLE  A +   +  FD</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KSFYHYLLKYRHPKPKDSISEFANQAYEDHSFPKTSTDYHEISSYLELNADYLHTMATFD</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>DIWEDY</entry><entry>68</entry></row><row><entry /><entry /><entry>+ W+ Y</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>EAWDQY</entry><entry>67</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 97&gt; which encodes the amino acid sequence &lt;SEQ ID 98&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00111" num="00111"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2571(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00112" num="00112"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 59/71 (83%), Positives = 65/71 (91%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MRKSFYSWLMTQRNPKSNEPVAILADYAFDETTFPKHSSDFETVSRYLEDEASFSFNLTD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MRKSFYSWLMTQRNPKSNEPVAILAD  FD+TTFPKH++DFE +SRYLED+ASFSFNL</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>MRKSFYSWLMTQRNPKSNEPVAILADLVFDDTTFPKHTNDFELISRYLEDQASFSFNLGQ</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>FDDIWEDYLNH</entry><entry>71</entry></row><row><entry /><entry /><entry>FD+IWEDYL H</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>FDEIWEDYLAH</entry><entry>73</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 32

A DNA sequence (GBSx0030) was identified in <i>S. agalactiae </i>&lt;SEQ ID 99&gt; which encodes the amino acid sequence &lt;SEQ ID 100&gt;. This protein is predicted to be antigen, 67 kDa (myosin-crossreactive). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00113" num="00113"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane</entry><entry>28-44 (26-45)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2826(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 101&gt; which encodes the amino acid sequence &lt;SEQ ID 102&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00114" num="00114"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 26</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.62</entry><entry>Transmembrane</entry><entry>40-56 (38-57)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2848(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related sequence was also identified in GAS &lt;SEQ ID 9109&gt; which encodes the amino acid sequence &lt;SEQ ID 9110&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00115" num="00115"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible cleavage site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.285(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00116" num="00116"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 477/590 (80%), Positives = 542/590 (91%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MRYTNGNFEAFARPRKPEGVDKKSAYIVGSGLAGLAAAVFLIRDGQMDGQRIHIFEELPL</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>M YT+GN+EAFA PRKPEGVD+KSAYIVG+GLAGLAAAVFLIRDG M G+RIH+FEELPL</entry></row><row><entry>Sbjct:</entry><entry>15</entry><entry>MYYTSGNYEAFATPRKPEGVDQKSAYIVGTGLAGLAAAVFLIRDGHMAGERIHLFEELPL</entry><entry>74</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>SGGSLDGVKRPDIGFVTRGGREMENHFECMWDMYRSIPSLEVPDASYLDEFYWLDKDDPN</entry><entry>122</entry></row><row><entry /><entry /><entry>+GGSLDG+++P +GFVTRGGREMENHFECMWDMYRSIPSLE+P ASYLDEFYWLDKDDPN</entry></row><row><entry>Sbjct:</entry><entry>75</entry><entry>AGGSLDGIEKPHLGFVTRGGREMENHFECMWDMYRSIPSLEIPGASYLDEFYWLDKDDPN</entry><entry>134</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>SSNCRLIHKQGNRLESDGDFTLGTHSKELVKLVMETEESLGAKTIEEVFSKEFFESNFWT</entry><entry>182</entry></row><row><entry /><entry /><entry>SSNCRLIHK+GNR++ DG +TLG  SKEL+ L+M+TEESLG +TIEE FS++FF+SNFW</entry></row><row><entry>Sbjct:</entry><entry>135</entry><entry>SSNCRLIHKRGNRVDDDGQYTLGKQSKELIHLIMKTEESLGDQTIEEFFSEDFFKSNFWV</entry><entry>194</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>YWGTMFAFEKWHSAIEMRRYAMRFIHHIGGLPDFTSLKFNKYNQYDSMVKPIISYLESHN</entry><entry>242</entry></row><row><entry /><entry /><entry>YW TMFAFEKWHSA+EMRRYAMRFIHHI GLPDFTSLKFNKYNQYDSMVKPII+YLESH+</entry></row><row><entry>Sbjct:</entry><entry>195</entry><entry>YWATMFAFEKWHSAVEMRRYAMRFIHHIDGLPDFTSLKFNKYNQYDSMVKPIIAYLESHD</entry><entry>254</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>VDVQFDSKVTNISVDFKNGQKLAKAIHLTVGGEAKTIDLTPNDFVFVTNGSITESTNYGS</entry><entry>302</entry></row><row><entry /><entry /><entry>VD+QFD+KVT+I V+   G+K+AK IH+TV GEAK I+LTP+D VFVTNGSITES+ YGS</entry></row><row><entry>Sbjct:</entry><entry>255</entry><entry>VDIQFDTKVTDIQVEQTAGKKVAKTIHMTVSGEAKAIELTPDDLVFVTNGSITESSTYGS</entry><entry>314</entry></row><row><entry /></row><row><entry>Query:</entry><entry>303</entry><entry>HDTVAKPNTDLGGSWNLWENLAAQSDEFGHPKVFYKDIPKESWFVSATATIKDPAIEPYI</entry><entry>362</entry></row><row><entry /><entry /><entry>H  VAKP   LGGSWNLWENLAAQSD+FGHPKVFY+D+P ESWFVSATATIK PAIEPYI</entry></row><row><entry>Sbjct:</entry><entry>315</entry><entry>HHEVAKPTKALGGSWNLWENLAAQSDDFGHPKVFYQDLPAESWFVSATATIKHPAIEPYI</entry><entry>374</entry></row><row><entry /></row><row><entry>Query:</entry><entry>363</entry><entry>ERLTHRDLHDGKVNTGGIVTVTDSNWMMSFAIHRQPHFKEQKENETIVWIYGLYSNVEGN</entry><entry>422</entry></row><row><entry /><entry /><entry>ERLTHRDLHDGKVNTGGI+T+TDSNWMMSFAIHRQPHFKEQKENET VWIYGLYSN EGN</entry></row><row><entry>Sbjct:</entry><entry>375</entry><entry>ERLTHRDLHDGKVNTGGIITITDSNWMMSFAIHRQPHFKEQKENETTVWIYGLYSNSEGN</entry><entry>434</entry></row><row><entry /></row><row><entry>Query:</entry><entry>423</entry><entry>YIKKPIEECTGREITEEWLYHLGVPEMKIHDLSDKQYVSTVPVYMPYITSYFMPRVKGDR</entry><entry>482</entry></row><row><entry /><entry /><entry>Y+ K IEECTG+EITEEWLYHLGVP  KI DL+ + Y++TVPVYMPYITSYFMPRVKGDR</entry></row><row><entry>Sbjct:</entry><entry>435</entry><entry>YVHKKIEECTGQEITEEWLYHLGVPVDKIKDLASQDYINTVPVYMPYITSYFMPRVKGDR</entry><entry>494</entry></row><row><entry /></row><row><entry>Query:</entry><entry>483</entry><entry>PDVIPQGSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVYTFLNIERGVPEVFNSAFDI</entry><entry>542</entry></row><row><entry /><entry /><entry>P VIP GSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVY+FLN+ERG+PEVFNSA+DI</entry></row><row><entry>Sbjct:</entry><entry>495</entry><entry>PKVIPDGSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVYSFLNVERGIPEVFNSAYDI</entry><entry>554</entry></row><row><entry /></row><row><entry>Query:</entry><entry>543</entry><entry>RVLLQSLYYLNDKKSVEDMDLPIPALMRKVGMKKIRGTYLEELLREAHLL</entry><entry>592</entry></row><row><entry /><entry /><entry>R LL++ YYLNDKK+++DMDLPIPAL+ K+G KKI+ T++EELL++A+L+</entry></row><row><entry>Sbjct:</entry><entry>555</entry><entry>RELLKAFYYLNDKKAIKDMDLPIPALIEKIGHKKIKDTFIEELLKDANLM</entry><entry>604</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8475&gt; and protein &lt;SEQ ID 8476&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00117" num="00117"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: −19.82</entry></row><row><entry>GvH: Signal Score (−7.5): −1.16</entry></row><row><entry>     Possible site: 14</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 1 value: −4.57 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="70pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane</entry><entry>26-42 (26-45)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 6.79</entry><entry>378</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 1.41</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.2826(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear)</entry></row></tbody></tgroup></table></tables>

SEQ ID 8476 (GBS90) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 18</figref> (lane 6; MW 68.5 kDa).

The GBS90-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 194</figref>, lane 11) and used to immunise mice. The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 256A</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 256B</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 33

A DNA sequence (GBSx0031) was identified in <i>S. agalactiae </i>&lt;SEQ ID 103&gt; which encodes the amino acid sequence &lt;SEQ ID 104&gt;. This protein is predicted to be phoh-like protein (phoH). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00118" num="00118"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2339(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00119" num="00119"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14476 GB: Z99117 phosphate starvation-induced protein</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 191/305 (62%), Positives = 241/305 (78%), Gaps = 1/305 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>27</entry><entry>LQHPDDMMSLFGSNERHLKLIEENLDVIIHARTERVQVLGDSEEAVETARLTIEALLVLV</entry><entry>86</entry><entry /></row><row><entry /><entry /><entry>L++PD+ +SLFG+ +  LKL+E++L++ I  R E + V GD +E+ + A   + +LL L+</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>LKNPDEALSLFGNQDSFLKLMEKDLNLNIITRGETIYVSGD-DESFQIADRLLGSLLALI</entry><entry>70</entry></row><row><entry /></row><row><entry>Query:</entry><entry>87</entry><entry>NRGMTVNTSDVVTALSMAQNGSIDKFVALYEEEIIKDSYGKPIRVKTLGQKIYVDSVKNH</entry><entry>146</entry></row><row><entry /><entry /><entry> +G+ ++  DV+ A+ MA+   ++ F ++YEEEI K++ GK IRVKT+GQ+ YV ++K +</entry></row><row><entry>Sbjct:</entry><entry>71</entry><entry>RKGIEISERDVIYAIKMAKKNELEYFESMYEEEITKNAKGKSIRVKTMGQREYVAAMKRN</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>147</entry><entry>DVVFGIGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPGDLKEKVDPY</entry><entry>206</entry></row><row><entry /><entry /><entry>D+VFGIGPAGTGKT+LAV  AV ALK G +K+IILTRPAVEAGESLGFLPGDLKEKVDPY</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>DLVFGIGPAGTGKTYLAVVKAVHALKNGHIKKIILTRPAVEAGESLGFLPGDLKEKVDPY</entry><entry>190</entry></row><row><entry /></row><row><entry>Query:</entry><entry>207</entry><entry>LRPVYDALYQILGKEQTSRLMEREIIEIAPLAYMRGRTLDDAFVILDEAQNTTIMQMKMF</entry><entry>266</entry></row><row><entry /><entry /><entry>LRP+YDAL+ +LG + T RLMER IIEIAPLAYMRGRTLDDA+VILDEAQNTT  QMKMF</entry></row><row><entry>Sbjct:</entry><entry>191</entry><entry>LRPLYDALHDVLGADHTERLMERGIIEIAPLAYMRGRTLDDAYVILDEAQNTTPAQMKMF</entry><entry>250</entry></row><row><entry /></row><row><entry>Query:</entry><entry>267</entry><entry>LTRLGFNSKMIVNGDVSQIDLPKNVKSGLIDAVEKLRNIKKIDFIHLSAKDVVRHPVVAE</entry><entry>326</entry></row><row><entry /><entry /><entry>LTRLGF+SKMI+ GDVSQIDLPK VKSGL  A E L+ I  I  I L   DVVRHP+VA+</entry></row><row><entry>Sbjct:</entry><entry>251</entry><entry>LTRLGFSSKMIITGDVSQIDLPKGVKSGLAVAKEMLKGIDGISMIELDQTDVVRHPLVAK</entry><entry>310</entry></row><row><entry /></row><row><entry>Query:</entry><entry>327</entry><entry>IINAY</entry><entry>331</entry></row><row><entry /><entry /><entry>II AY</entry></row><row><entry>Sbjct:</entry><entry>311</entry><entry>IIEAY</entry><entry>315</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 105&gt; which encodes the amino acid sequence &lt;SEQ ID 106&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00120" num="00120"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 42</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.85</entry><entry>Transmembrane</entry><entry>54-70 (54-70)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1341(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00121" num="00121"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 274/322 (85%), Positives = 298/322 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>18</entry><entry>LQEYSIEITLQHPDDMMSLFGSNERHLKLIEENLDVIIHARTERVQVLGDSEEAVETARL</entry><entry>77</entry><entry /></row><row><entry /><entry /><entry>LQEYSI+ITL HPDD+++LFGSNERHLKLIE +L VI+HARTERVQV+GD EEAVE ARL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LQEYSIDITLTHPDDVLALFGSNERHLKLIEAHLGVIVHARTERVQVIGDDEEAVELARL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>78</entry><entry>TIEALLVLVNRGMTVNTSDVVTALSMAQNGSIDKFVALYEEEIIKDSYGKPIRVKTLGQK</entry><entry>137</entry></row><row><entry /><entry /><entry>TI+ALLVLV RGM VNTSDVVTALSMA++  ID+F+ALYEEEIIKD+YGK IRVKTLGQK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TIKALLVLVGRGMVVNTSDVVTALSMAESHQIDQFMALYEEEIIKDNYGKAIRVKTLGQK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>138</entry><entry>IYVDSVKNHDVVFGIGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG</entry><entry>197</entry></row><row><entry /><entry /><entry> YVDSVK HDVVFG+GPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TYVDSVKRHDVVFGVGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>198</entry><entry>DLKEKVDPYLRPVYDALYQILGKEQTSRLMEREIIEIAPLAYMRGRTLDDAFVILDEAQN</entry><entry>257</entry></row><row><entry /><entry /><entry>DLKEKVDPYLRPVYDALY ILGKEQT+RLMER++IEIAPLAYMRGRTLDDAFVILDEAQN</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>DLKEKVDPYLRPVYDALYHILGKEQTTRLMERDVIEIAPLAYMRGRTLDDAFVILDEAQN</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>258</entry><entry>TTIMQMKMFLTRLGFNSKMIVNGDVSQIDLPKNVKSGLIDAVEKLRNIKKIDFIHLSAKD</entry><entry>317</entry></row><row><entry /><entry /><entry>TTIMQMKMFLTRLGFNSKMIVNGD SQIDLP+NVKSGLIDA +KL+ IK+IDF++ SAKD</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>TTIMQMKMFLTRLGFNSKMIVNGDTSQIDLPRNVKSGLIDATQKLQGIKQIDFVYFSAKD</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>318</entry><entry>VVRHPVVAEIINAYSDSESSHK</entry><entry>339</entry></row><row><entry /><entry /><entry>VVRHPVVA+II AY  S    K</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>VVRHPVVADIIKAYETSSEEMMK</entry><entry>322</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 34

A DNA sequence (GBSx0032) was identified in <i>S. agalactiae </i>&lt;SEQ ID 107&gt; which encodes the amino acid sequence &lt;SEQ ID 108&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00122" num="00122"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0275(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 35

A DNA sequence (GBSx0033) was identified in <i>S. agalactiae </i>&lt;SEQ ID 109&gt; which encodes the amino acid sequence &lt;SEQ ID 110&gt;. This protein is predicted to be MutT/nudix family protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00123" num="00123"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2383(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00124" num="00124"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;Gp: AAF09597 GB: AE001864 MutT/nudix family</entry><entry /></row><row><entry>protein [<i>Deinococcus radiodurans</i>]</entry></row><row><entry>Identities = 49/136 (36%), Positives = 69/136 (50%), Gaps = 8/136 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>YISYIRSKVGHETIFLTYSGGILTDGKGRVLLQLRADKNSWGIIGGCMELGESSVDTLKR</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>Y+S +R+  GH  +       +L D  GRVLLQ R D   WGI+GG +E GE  +    R</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>YLSELRAVWGHRALPAAGVSVLLQDETGRVLLQRRGDDGQWGILGGGLEPGEDFLIAAHR</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>EFFEETGLRVEPIRLLNVY------TNFQDSYPNGDKAQTVGFIYEVSCPKPVNIEGFHN</entry><entry>118</entry></row><row><entry /><entry /><entry>E  EETGLR   +R L +         F   YPNGD+   VG   E + P     +   +</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>ELLEETGLRCPNLRPLPLSEGLVSGPQFWHRYPNGDEVYLVGLRTEGTVPAAALTDACPD</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>E--ETLQLDYFSKEDV</entry><entry>132</entry></row><row><entry /><entry /><entry>+  ETL+L +F+ +D+</entry></row><row><entry>Sbjct:</entry><entry>126</entry><entry>DGGETLELRWFALDDL</entry><entry>141</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 111&gt; which encodes the amino acid sequence &lt;SEQ ID 112&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00125" num="00125"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4375(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00126" num="00126"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 93/157 (59%), Positives = 123/157 (78%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKQDYISYIRSKVGHETIFLTYSGGILTDGKGRVLLQLRADKNSWGIIGGCMELGESSVD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M QDYISYIRSKVGH+ I L ++GGILT+  G+VL+QLR DK +W I GG MELGESS++</entry></row><row><entry>Sbjct:</entry><entry>16</entry><entry>MPQDYISYIRSKVGHDKIILNFAGGILTNDDGKVLMQLRGDKKTWTIPGGTMELGESSLE</entry><entry>75</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TLKREFFEETGLRVEPIRLLNVYTNFQDSYPNGDKAQTVGFIYEVSCPKPVNIEGFHNEE</entry><entry>120</entry></row><row><entry /><entry /><entry>T KREF EETG+ VE +RLLNVYT+F++ YPNGD  QT+ FIYE++    + I+ FHNEE</entry></row><row><entry>Sbjct:</entry><entry>76</entry><entry>TCKREFLEETGIEVEAVRLLNVYTHFEEVYPNGDAVQTIVFIYELTAVSDMAIDNFHNEE</entry><entry>135</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TLQLDYFSKEDVKNITIVNEQHQLILDEYFSQTFQMG</entry><entry>157</entry></row><row><entry /><entry /><entry>TL+L +FS E++  +  V+ +H+L+L+EYFS +F MG</entry></row><row><entry>Sbjct:</entry><entry>136</entry><entry>TLKLQFFSHEEIAELESVSAKHRLMLEEYFSDSFAMG</entry><entry>172</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 36

A DNA sequence (GBSx0034) was identified in <i>S. agalactiae </i>&lt;SEQ ID 113&gt; which encodes the amino acid sequence &lt;SEQ ID 114&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00127" num="00127"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3690 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 37

A DNA sequence (GBSx0035) was identified in <i>S. agalactiae </i>&lt;SEQ ID 115&gt; which encodes the amino acid sequence &lt;SEQ ID 116&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00128" num="00128"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>             bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>            bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00129" num="00129"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAG05249 GB:AE004612 hypothetical protein [<i>Pseudomonas aeruginosa</i>]</entry><entry /></row><row><entry>Identities = 70/254 (27%), Positives = 127/254 (49%), Gaps = 2/254 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>KITLHGVAETLLITLYIRAKDAMAKHPILNDQKSLAIVEQIEYDFDKFDNSEASFYATLA</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+ITL G  +TLLITLY +A D+     IL+D+ +   V QI++DF +    + +  A</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>RITLTGEKQTLLITLYAKALDSRLDDSILHDRFAEEAVRQIDFDFSRVALGKGNERALAM</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>RIRVMDREIKKFIRENPNSQILSIGCGLDTRFERVD-NGQIRWYNLDLPEVMEIRKLFFE</entry><entry>120</entry></row><row><entry /><entry /><entry>R    D+  ++F+  +P  Q+L++GCGLD+R  RVD   ++ W++LD PEVM++R+  +</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>RSHYFDQACREFLGRHPEGQVLNLGCGLDSRIYRVDPPAELPWFDLDYPEVMDLRERLYP</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>EHERVTNIAKSALDETWTREVNPQNAPFLIVSEGVLMFLKEDDVETFLHILTNSFSQFMA</entry><entry>180</entry></row><row><entry /><entry /><entry>         + ++D+    +  P+  P L+++EG++ +L+E  V   +  L +</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>PRAGAYRALRHSVDDDGWLQGVPRERPALVLAEGLMPYLRESQVRRLVERLVDHLGSGEL</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>QFDLCHKEMINKGKQHDTVKYMDTEFQFGITDGHEIVDLDPKLKQINLINFTDEMSKFEL</entry><entry>240</entry></row><row><entry /><entry /><entry> FD   +  I   + +  ++    +  + I D  E+    P L+ I  +   D     +L</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>LFDGYGRLGIMLLRLYPPLRETGAQVHWSIDDPRELERWHPALRFIEEVTDYDPQDVAKL</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>-GTLRSLLPTIRKF</entry><entry>253</entry></row><row><entry /><entry /><entry>  + R +LP    F</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>PQSSRLMLPIYNGF</entry><entry>258</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8477&gt; and protein &lt;SEQ ID 8478&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00130" num="00130"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 9</entry><entry /></row><row><entry>McG: Discrim Score: 0.37</entry></row><row><entry>GvH: Signal Score (−7.5): −0.97</entry></row><row><entry>Possible site: 25</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="91pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="189pt" align="left" /><colspec colname="4" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>ALOM program count: 0</entry><entry>value: 4.35</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="189pt" align="left" /><colspec colname="4" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 4.35</entry><entry>143</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −1.37</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm ---Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00008" num="00008"><img id="EMI-C00008" he="98.13mm" wi="118.79mm" file="US07939087-20110510-C00008.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00008" attachment-type="cdx" file="US07939087-20110510-C00008.CDX" /><attachment idref="CHEM-US-00008" attachment-type="mol" file="US07939087-20110510-C00008.MOL" /></attachments></chemistry>

SEQ ID 8478 (GBS176) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 36</figref> (lane 5 &amp; 6; MW 30 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 41</figref> (lane 7; MW 55.4 kDa).

The GBS176-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 117A</figref>; see also <figref idrefs="DRAWINGS">FIG. 202</figref>, lane 5) and used to immunise mice (lane 1+2 product; 13.5 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 117B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 117C</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 38

A DNA sequence (GBSx0036) was identified in <i>S. agalactiae </i>&lt;SEQ ID 117&gt; which encodes the amino acid sequence &lt;SEQ ID 118&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00131" num="00131"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3712(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 10019&gt; which encodes amino acid sequence &lt;SEQ ID 10020&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00132" num="00132"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC38046 GB: AF000954 No definition line found [<i>Streptococcus mutans</i>]</entry><entry /></row><row><entry>Identities = 140/164 (85%), Positives = 157/164 (95%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYVEMIDETGQVSEDIKKQTLDLLEFAAQKTGKENKEMAVTFVTNERSHELNLEYRDTDR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MY+EMIDET QVSE IK QTLD+LEFAAQKTGKE+KEMAVTFVTNERSHELNL+YRDT+R</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MYIEMIDETNQVSEGIKNQTLDILEFAAQKTGKEDKEMAVTFVTNERSHELNLKYRDTNR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>PTDVISLEYKPEVDISFDEEDLAENPELAEMLEDFDSYIGELFISIDKAKEQAEEYGHSY</entry><entry>120</entry></row><row><entry /><entry /><entry>PTDVISLEYKPE  +SFDEEDLA++P+LAE+L +FD+YIGELFIS+DKA+EQA+EYGHS+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PTDVISLEYKPESSLSFDEEDLADDPDLAEVLTEFDAYIGELFISVDKAREQAQEYGHSF</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>EREMGFLAVHGFLHINGYDHYTPEEEKEMFSLQEEILTAYGLKR</entry><entry>164</entry></row><row><entry /><entry /><entry>EREMGFLAVHGFLHINGYDHYTP+EEKEMFSLQEEIL AYGLKR</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>EREMGFLAVHGFLHINGYDHYTPQEEKEMFSLQEEILDAYGLKR</entry><entry>164</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 119&gt; which encodes the amino acid sequence &lt;SEQ ID 120&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00133" num="00133"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1145(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00134" num="00134"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 138/165 (83%), Positives = 153/165 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYVEMIDETGQVSEDIKKQTLDLLEFAAQKTGKENKEMAVTFVTNERSHELNLEYRDTDR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MY+EMIDETGQVS++I +QTLDLL FAAQKTGKE KEM+VTFVTNERSHELNLEYRDTDR</entry></row><row><entry>Sbjct:</entry><entry>18</entry><entry>MYIEMIDETGQVSQEIMEQTLDLLNFAAQKTGKEEKEMSVTFVTNERSHELNLEYRDTDR</entry><entry>77</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>PTDVISLEYKPEVDISFDEEDLAENPELAEMLEDFDSYIGELFISIDKAKEQAEEYGHSY</entry><entry>120</entry></row><row><entry /><entry /><entry>PTDVISLEYKPE  I F +EDLA +P LAEM+ +FD+YIGELFISIDKA+EQ++EYGHS+</entry></row><row><entry>Sbjct:</entry><entry>78</entry><entry>PTDVISLEYKPETPILFSQEDLAADPSLAEMMAEFDAYIGELFISIDKAREQSQEYGHSF</entry><entry>137</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>EREMGFLAVHGFLHINGYDHYTPEEEKEMFSLQEEILTAYGLKRQ</entry><entry>165</entry></row><row><entry /><entry /><entry>EREMGFLAVHGFLHINGYDHYT EEEKEMF+LQEEILTAYGL RQ</entry></row><row><entry>Sbjct:</entry><entry>138</entry><entry>EREMGFLAVHGFLHINGYDHYTLEEEKEMFTLQEEILTAYGLTRQ</entry><entry>182</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 39

A DNA sequence (GBSx0038) was identified in <i>S. agalactiae </i>&lt;SEQ ID 121&gt; which encodes the amino acid sequence &lt;SEQ ID 122&gt;. This protein is predicted to be phosphoglycerate dehydrogenase (serA) (serA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00135" num="00135"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2817(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00136" num="00136"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAB99020 GB:U67544 phosphoglycerate dehydrogenase (serA)</entry><entry /></row><row><entry>[<i>Methanococcus jannaschii</i>]</entry></row><row><entry>Identities = 82/232 (35%), Positives = 132/232 (56%),</entry></row><row><entry>Gaps = 14/232 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>ENPDAYIIRSQNLHNQDF---PSNLKAIARAGAGTNNIPIEEASAQGIVVFNTPGANANA</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>++ D  ++RS     +D       LK I RAG G +NI +E A+ +GI+V N P A++ +</entry></row><row><entry>Sbjct:</entry><entry>40</entry><entry>KDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSIS</entry><entry>99</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>VKEAVIAALLLSARDYLGANRWVNTLTGTDIPKQIEAGKKAFAGNEIAGKKLGVIGLGAI</entry><entry>119</entry></row><row><entry /><entry /><entry>V E  +  +L +AR         N    T   K+ E  +K F G E+ GK LGVIGLG I</entry></row><row><entry>Sbjct:</entry><entry>100</entry><entry>VAELTMGLMLAAAR---------NIPQATASLKRGEWDRKRFKGIELYGKTLGVIGLGRI</entry><entry>150</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>GARIANDARRLGMTVLGYDPYVSIETAWNISSHVQRVKEIKDIFETCDYITIHVPLTNET</entry><entry>179</entry></row><row><entry /><entry /><entry>G ++   A+  GM ++GYDPY+  E A ++   V+ V +I ++ +  D+IT+HVPLT +T</entry></row><row><entry>Sbjct:</entry><entry>151</entry><entry>GQQVVKRAKAFGMNIIGYDPYIPKEVAESMG--VELVDDINELCKRADFITLHVPLTPKT</entry><entry>208</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>KHTFDAKAFSIMKKGTTIINFARAELVNNQELFEAIETGVVKRYITDFGDKE</entry><entry>231</entry></row><row><entry /><entry /><entry>+H    +  ++MKK   I+N AR  L++ + L+EA++ G ++    D  ++E</entry></row><row><entry>Sbjct:</entry><entry>209</entry><entry>RHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEE</entry><entry>260</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 123&gt; which encodes the amino acid sequence &lt;SEQ ID 124&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00137" num="00137"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 52</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2384(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00138" num="00138"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 52/198 (26%), Positives = 93/198 (46%), Gaps = 14/198 (7%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="left" /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>24</entry><entry>LKAIARAGAGTNNIPIEEASAQGIVVFNTPGANANAVKEAVIAALLLSARDYLGANRWVN</entry><entry>83</entry><entry /></row><row><entry /><entry /><entry>+K IA+  A  +   ++ A+   I++ N P  +  ++ E  +  +L   R</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>IKQIAQHSASVDMYNLDLATENDIIITNVPSYSPESIAEFTVTIVLNLIRHV--------</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>84</entry><entry>TLTGTDIPKQIEAGKKAFAGNEIAGKKLGVIGLGAIGARIANDARRLGMTVLGYDPYVSI</entry><entry>143</entry></row><row><entry /><entry /><entry> L   ++ KQ         G  +    + +IG G IG   A   +  G  V+GYD Y S</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>ELIRENVKKQNFTWGLPIRGRVLGDMTVAIIGTGRIGLATAKIFKGFGCKVVGYDIYQS-</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>144</entry><entry>ETAWNISSHVQRVKE-IKDIFETCDYITIHVPLTNETKHTFDAKAFSIMKKGTTIINFAR</entry><entry>202</entry></row><row><entry /><entry /><entry>+ A  +  + + V+E IKD     D +++H+P T E  H F++  F   KKG  ++N AR</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>DAAKAVLDYKESVEEAIKD----ADLVSLHMPPTAENTHLFNSDLFKSFKKGAILMNMAR</entry><entry>236</entry></row><row><entry /></row><row><entry>Query:</entry><entry>203</entry><entry>AELVNNQELFEAIETGVV</entry><entry>220</entry></row><row><entry /><entry /><entry>  ++  Q+L +A++ G++</entry></row><row><entry>Sbjct:</entry><entry>237</entry><entry>GAVIETQDLLDALDAGLL</entry><entry>254</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 40

A DNA sequence (GBSx0039) was identified in <i>S. agalactiae </i>&lt;SEQ ID 125&gt; which encodes the amino acid sequence &lt;SEQ ID 126&gt;. This protein is predicted to be alpha-glycerophosphate oxidase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00139" num="00139"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2067(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00140" num="00140"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC34740 GB:U94770 alpha-glycerophosphate oxidase [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 24/49 (48%), Positives = 37/49 (74%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLFMRDNLDSLIQPVIDEMAKHYQWSDQDKTFYEEELHETLKDNDLAAL</entry><entry>49</entry><entry /></row><row><entry /><entry /><entry>MLFMRD+LDS+++PV+DEM + Y W++++K  Y  ++   L +NDLA L</entry></row><row><entry>Sbjct:</entry><entry>558</entry><entry>MLFMRDSLDSIVEPVLDEMGRFYDWTEEEKATYRADVEAALANNDLAEL</entry><entry>606</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 127&gt; which encodes the amino acid sequence &lt;SEQ ID 128&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00141" num="00141"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.81</entry><entry>Transmembrane</entry><entry>20-36 (20-36)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1723(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00142" num="00142"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC34740 GB: U94770 alpha-glycerophosphate oxidase</entry><entry /></row><row><entry>[<i>Streptococcus pneumonia</i>]</entry></row><row><entry>Identities = 462/607 (76%), Positives = 539/607 (88%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEFSRETRRLALQKMQERDLDLLIIGGGITGAGVALQAAASGLDTGLIEMQDFAQGTSSR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MEFS++TR L+++KMQER LDLLIIGGGITGAGVALQAAASGL+TGLIEMQDFA+GTSSR</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MEFSKKTRELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEPGSTFSMFRL</entry><entry>120</entry></row><row><entry /><entry /><entry>STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDE G+TFS+FRL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEDGATFSLFRL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>KVAMDLYDLLAGVSNTPAANKVLTKEEVLKREPDLKQEGLLGGGVYLDFRNNDARLVIEN</entry><entry>180</entry></row><row><entry /><entry /><entry>KVAMDLYDLLAGVSNTP ANKVL+K++VL+R+P+LK+EGL+GGGVYLDFRNNDARLVIEN</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>KVAMDLYDLLAGVSNTPTANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIEN</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>IKRANRDGALIASHVKAEDFLLDDNGKIIGVKARDLLSDQEIIIKAKLVINTTGPWSDEI</entry><entry>240</entry></row><row><entry /><entry /><entry>IKRAN+DGALIA+HVKAE FL D++GKI GV ARDLL+DQ   IKA+LVINTTGPWSD++</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>IKRANQDGALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>RQFSHKGQPIHQMRPTKGVHLVVDRQKLPVSQPVYVDTGLNDGRMVFVLPREEKTYFGTT</entry><entry>300</entry></row><row><entry /><entry /><entry>R  S+KG    QMRPTKGVHLVVD  K+ VSQPVY DTGL DGRMVFVLPRE KTYFGTT</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>RNLSNKGTQFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTT</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>DTDYTGDLEHPQVTQEDVDYLLGVVNNRFPNANVTIDDIESSWAGLRPLLSGNSASDYNG</entry><entry>360</entry></row><row><entry /><entry /><entry>DTDYTGDLEHP+VTQEDVDYLLG+VNNRFP +N+TIDDIESSWAGLRPL++GNSASDYNG</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>DTDYTGDLEHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNG</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>GNSGKVSDDSFDHLVDTVKAYINHEDSREAVEKAIKQVETSTSEKELDPSAVSRGSSFER</entry><entry>420</entry></row><row><entry /><entry /><entry>GN+G +SD+SFD+L+ TV++Y++ E +RE VE A+ ++E+STSEK LDPSAVSRGSS +R</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GNNGTISDESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDR</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>DENGLFTLAGGKITDYRKMAEGALTGIIQILKEEFGKSFKLINSKTYPVSGGEINPANVD</entry><entry>480</entry></row><row><entry /><entry /><entry>D+NGL TLAGGKITDYRKMAEGA+  ++ ILK EF +SFKLINSKTYPVSGGE+NPANVD</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>DDNGLLTLAGGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVD</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>SEIEAYAQLGTLSGLSMDDARYLANLYGSNAPKVFALTRQLTAAEGLSLAETLSLHYAMD</entry><entry>540</entry></row><row><entry /><entry /><entry>SEIEA+AQLG   GL   +A YLANLYGSNAPKVFAL   L  A GLSLA+TLSLHYAM</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>SEIEAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLSLHYAMR</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>YEMALKPTDYFLRRTNHLLFMRDSLDALIDPVINEMAKHFEWSDQERVAQEDDLRRVIAD</entry><entry>600</entry></row><row><entry /><entry /><entry> E+AL P D+ LRRTNH+LFMRDSLD++++PV++EM + ++W+++E+     D+   +A+</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>NELALSPVDFLLRRTNHMLFMRDSLDSIVEPVLDEMGRFYDWTEEEKATYRADVEAALAN</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>NDLSALK</entry><entry>607</entry></row><row><entry /><entry /><entry>NDL+ LK</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>NDLAELK</entry><entry>607</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00143" num="00143"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="266pt" align="left" /><colspec colname="2" colwidth="175pt" align="left" /><tbody valign="top"><row><entry>Identities = 29/49 (59%), Positives = 41/49 (83%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="210pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="175pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLFMRDNLDSLIQPVIDEMAKHYQWSDQDKTFYEEELHETLKDNDLAAL</entry><entry>49</entry><entry /></row><row><entry /><entry /><entry>+LFMRD+LD+LI PVI+EMAKH++WSDQ++   E++L   + DNDL+AL</entry></row><row><entry>Sbjct:</entry><entry>558</entry><entry>LLFMRDSLDALIDPVINEMAKHFEWSDQERVAQEDDLRRVIADNDLSAL</entry><entry>606</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 41

A DNA sequence (GBSx0040) was identified in <i>S. agalactiae </i>&lt;SEQ ID 129&gt; which encodes the amino acid sequence &lt;SEQ ID 130&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00144" num="00144"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1011(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00145" num="00145"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06309 GB: AP001516 unknown conserved protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 70/160 (43%), Positives = 106/160 (65%), Gaps = 3/160 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>TRPTTDKVKGAIFNMIGPFFEGGRVLDLFSGSGSLAIEAISRGMDQAVLVEKDRRAQVVI</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>TRPTTDKVK AIFNMIGPFF+GG  LDL+ GSG L IEA+SRG+++ + V++ +RA   I</entry></row><row><entry>Sbjct:</entry><entry>21</entry><entry>TRPTTDKVKEAIFNMIGPFFDGGIGLDLYGGSGGLGIEALSRGVERMIFVDQQKRAIETI</entry><entry>80</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>QENIAMTKSPEQFQLLKMEANRALEQLTGQ---FDLVLLDPPYAKEEIVKQIQIMDSKGL</entry><entry>121</entry></row><row><entry /><entry /><entry>++N++      + ++ + +A RAL+ LT +   F  V LDPPYAK+ I   + I+ + GL</entry></row><row><entry>Sbjct:</entry><entry>81</entry><entry>KQNLSHCGLEGRAEVYRNDAKRALQVLTKRGIVFAYVFLDPPYAKQTIKNDLAILANHGL</entry><entry>140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>LGDDIMIACETDKSVDLPEEIASFGIWKQKIYGISKVTVY</entry><entry>161</entry></row><row><entry /><entry /><entry>L +  ++ CE D+   LP++I      K++ YG + +T+Y</entry></row><row><entry>Sbjct:</entry><entry>141</entry><entry>LEEGGVVVCEHDRDTMLPDQIEYAVKHKEETYGDTMITIY</entry><entry>180</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 131&gt; which encodes the amino acid sequence &lt;SEQ ID 132&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00146" num="00146"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3814(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00147" num="00147"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 111/160 (69%), Positives = 136/160 (84%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>RTTRPTTDKVKGAIFNMIGPFFEGGRVLDLFSGSGSLAIEAISRGMDQAVLVEKDRRAQV</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>+ TRPT+DKV+GAIFNMIGP+F GGRVLDLF+GSG LAIEA+SRGM  AVLVEK+R+AQ</entry></row><row><entry>Sbjct:</entry><entry>19</entry><entry>KITRPTSDKVRGAIFNMIGPYFNGGRVLDLFAGSGGLAIEAVSRGMSAAVLVEKNRKAQA</entry><entry>78</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>VIQENIAMTKSPEQFQLLKMEANRALEQLTGQFDLVLLDPPYAKEEIVKQIQIMDSKGLL</entry><entry>122</entry></row><row><entry /><entry /><entry>+IQ+NI MTK+  +F LLKMEA RA++ LTG+FDLV LDPPYAKE IV  I+ + +K LL</entry></row><row><entry>Sbjct:</entry><entry>79</entry><entry>IIQDNIIMTKAENRFTLLKMEAERAIDCLTGRFDLVFLDPPYAKETIVATIEALAAKNLL</entry><entry>138</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>GDDIMIACETDKSVDLPEEIASFGIWKQKIYGISKVTVYV</entry><entry>162</entry></row><row><entry /><entry /><entry> + +M+ CETDK+V LP+EIA+ GIWK+KIYGISKVTVYV</entry></row><row><entry>Sbjct:</entry><entry>139</entry><entry>SEQVMVVCETDKTVLLPKEIATLGIWKEKIYGISKVTVYV</entry><entry>178</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 42

A DNA sequence (GBSx0041) was identified in <i>S. agalactiae </i>&lt;SEQ ID 133&gt; which encodes the amino acid sequence &lt;SEQ ID 134&gt;. This protein is predicted to be lipopolysaccharide core biosynthesis protein kdtB (kdtB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00148" num="00148"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1937(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00149" num="00149"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB13272 GB:AP001119 lipopolysaccharide core biosynthesis</entry><entry /></row><row><entry>protein kdtB [<i>Buchnera </i>sp. APS]</entry></row><row><entry>Identities = 56/149 (37%), Positives = 94/149 (62%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTKKALFTGSFDPVTNGHLDIIERASYLFDHVYIGLFYNLEKQGYFSIECRKKMLEEAIR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M K A++ G+FDP+T GHLDII RA+ +FD + I +  N  K+  F+++ R ++  +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNKTAIYPGTFDPITYGHLDIITRATKIFDSITIAISNNFTKKPIFNLKERIELTRKVTL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QFKNVSVLVAQDRLAVDLAREVGAKYFVRGLRNSQDFDYEANLEFFNKQLADDIETVYLS</entry><entry>120</entry></row><row><entry /><entry /><entry>  KNV  ++  + L  +LA++  A   +RG+R   DFDYE  L   NKQ+  D+++++L</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>HLKNVKKILGFNDLLANLAKKEKANILIRGVRTIFDFDYEIKLAAINKQIYPDLDSIFLL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TSPSLSPISSSRIRELIHFKASVKPFVPK</entry><entry>149</entry></row><row><entry /><entry /><entry>+S  +S ISSS ++E+  +K  +KP++PK</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SSKEVSFISSSFVKEIAKYKGDIKPYLPK</entry><entry>149</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 135&gt; which encodes the amino acid sequence &lt;SEQ ID 136&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00150" num="00150"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1862(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00151" num="00151"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 88/161 (54%), Positives = 124/161 (76%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTKKALFTGSFDPVTNGHLDIIERASYLFDHVYIGLFYNLEKQGYFSIECRKKMLEEAIR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+TK  L+TGSFDPVTNGHLDI++RAS LFD +Y+G+F N  K+ YF +E RK ML +A+</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>LTKIGLYTGSFDPVTNGHLDIVKRASGLFDQIYVGIFDNPTKKSYFKLEVRKAMLTQALA</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QFKNVSVLVAQDRLAVDLAREVGAKYFVRGLRNSQDFDYEANLEFFNKQLADDIETVYLS</entry><entry>120</entry></row><row><entry /><entry /><entry> F NV V+ + +RLA+D+A+E+   + +RGLRN+ DF+YE NLE+FN  LA +IETVYL</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>DFTNVIVVTSHERLAIDVAKELRVTHLIRGLRNATDFEYEENLEYFNHLLAPNIETVYLI</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TSPSLSPISSSRIRELIHFKASVKPFVPKSVVREVEKMSEE</entry><entry>161</entry></row><row><entry /><entry /><entry>+      +SSSR+RELIHF++S++  VP+SV+ +VEKM+E+</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>SRNKWQALSSSRVRELIHFQSSLEGLVPQSVIAQVEKMNEK</entry><entry>162</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 43

A DNA sequence (GBSx0042) was identified in <i>S. agalactiae </i>&lt;SEQ ID 137&gt; which encodes the amino acid sequence &lt;SEQ ID 138&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00152" num="00152"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1126(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 44

A DNA sequence (GBSx0043) was identified in <i>S. agalactiae </i>&lt;SEQ ID 139&gt; which encodes the amino acid sequence &lt;SEQ ID 140&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00153" num="00153"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.04</entry><entry>Transmembrane</entry><entry>20-36 (12-43)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5416(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00154" num="00154"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB13378 GB:Z99111 ylbL [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 124/344 (36%), Positives = 199/344 (57%), Gaps = 21/344 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>20</entry><entry>WIIGFAFLLLVLASLVVRLPYYLEMPGGAYDIRSVLKVNKKADKAKGSYNFVAVSVSQAT</entry><entry>79</entry><entry /></row><row><entry /><entry /><entry>W++    L+ VL+   ++LPYY+  PG A ++ S++KV     + KGS + + V V  A</entry></row><row><entry>Sbjct:</entry><entry>9</entry><entry>WMLVILILIAVLS--FIKLPYYITKPGEATELASLIKVEGGYPE-KGSLSLMTVKVGPAN</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>80</entry><entry>PAQVLYAWLTPFTEL----SSKEETTGGFSNDDYLRINQFYMETSQNESIYQALKLANKQ</entry><entry>135</entry></row><row><entry /><entry /><entry>P   ++A + P+ E+    S KEE   G S+ +Y++     M++SQ  ++  A + A K+</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>PFTYVWAKMHPYYEIVPDESIKEE---GESDKEYMKRQLQMMKSSQENAVIAAYQKAGKK</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>136</entry><entry>VSLTYKGVYVLNLAKNSTFKDRLHLADTVTGVNGKSFKNSSQLIKYVAALHLGDKVKVQY</entry><entry>195</entry></row><row><entry /><entry /><entry>VS ++ G+Y  ++ +N   K ++ + D +   +GK+++++ +LI Y+++   GDKV ++</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>VSYSFNGIYASSVVENMPAKGKIEVGDKIISADGKNYQSAEKLIDYISSKKAGDKVTLKI</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>196</entry><entry>TSQGKKKESVGKVIKLSNGKNGIGIGLTDHTE--VLSDVPVDFNTEGVGGPSAGLMFTLA</entry><entry>253</entry></row><row><entry /><entry /><entry>  + K+K     + +  +  +  GIG++ +T+  V  +  +DF  E +GGPSAGLM +L</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>EREEKEKRVTLTLKQFPDEPDRAGIGVSLYTDRNVKVEPDIDFEIENIGGPSAGLMMSLE</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>254</entry><entry>IYDQLVKEDLRKGRKIAGTGTIEQNGHVGDIGGAGLKVVSAAKKGMDIFFVPNNPIDKNA</entry><entry>313</entry></row><row><entry /><entry /><entry>IY+QL K D  KG  IAGTGTI+ +G VG IGG   KVV+A K G DIFF PN     N</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>IYNQLTKPDETKGYDIAGTGTIDVDGKVGPIGGIDQKVVAADKAGKDIFFAPNQNGASN-</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>314</entry><entry>KKGKTKVQTNYQEAKAAAKRLGTKMKIVPVQNVQQAIDYLKKTK</entry><entry>357</entry></row><row><entry /><entry /><entry>        ++Y+ A   AK + + MKIVPV  +Q AIDYL K K</entry></row><row><entry>Sbjct:</entry><entry>302</entry><entry>--------SDYKNAVKTAKDIDSNMKIVPVDTMQDAIDYLNKLK</entry><entry>337</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 141&gt; which encodes the amino acid sequence &lt;SEQ ID 142&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00155" num="00155"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.24</entry><entry>Transmembrane</entry><entry>10-26 (6-34)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5097(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00156" num="00156"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB13378 GB:Z99111 ylbL [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 132/348 (37%), Positives = 198/348 (55%), Gaps = 16/348 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKRLKKIKWWLVGLLALISLLLALFFPLPYYIEMPGGAYDIRTVLQVNGKEDKRKGAYQF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M R K   W LV +L LI++L   F  LPYYI  PG A ++ ++++V G   + KG+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLRKKHFSWMLV-ILILIAVLS--FIKLPYYITKPGEATELASLIKVEGGYPE-KGSLSL</entry><entry>56</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VAVGISRASLAQLLYAWLTPFTEISTAEDTTG-GYSDADFLRINQFYMETSQNAAIYQAL</entry><entry>119</entry></row><row><entry /><entry /><entry>+ V +  A+    ++A + P+ EI   E     G SD ++++     M++SQ  A+  A</entry></row><row><entry>Sbjct:</entry><entry>57</entry><entry>MTVKVGPANPFTYVWAKMHPYYEIVPDESIKEEGESDKEYMKRQLQMMKSSQENAVIAAY</entry><entry>116</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>SLAGKPVTLDYKGVYVLDVNNESTFKGTLHLADTVTGVNGKQFTSSAELIDYVSHLKLGD</entry><entry>179</entry></row><row><entry /><entry /><entry>  AGK V+  + G+Y   V      KG + + D +   +GK + S+ +LIDY+S  K GD</entry></row><row><entry>Sbjct:</entry><entry>117</entry><entry>QKAGKKVSYSFNGIYASSVVENMPAKGKIEVGDKIISADGKNYQSAEKLIDYISSKKAGD</entry><entry>176</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>EVTVQFTSDNKPKKGVGRIIKLKN--GKNGIGIALTDHTSVNSEDTVIFSTKGVGGPSAG</entry><entry>237</entry></row><row><entry /><entry /><entry>+VT++   + K K+    + +  +   + GIG++L    +V  E  + F  + +GGPSAG</entry></row><row><entry>Sbjct:</entry><entry>177</entry><entry>KVTLKIEREEKEKRVTLTLKQFPDEPDRAGIGVSLYTDRNVKVEPDIDFEIENIGGPSAG</entry><entry>236</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>LMFTLDIYDQITKEDLRKGRTIAGTGTIGKDGEVGDIGGAGLKVVAAAEAGADIFFVPNN</entry><entry>297</entry></row><row><entry /><entry /><entry>LM +L+IY+Q+TK D  KG  IAGTGTI  DG+VG IGG   KVVAA +AG DIFF PN</entry></row><row><entry>Sbjct:</entry><entry>237</entry><entry>LMMSLEIYNQLTKPDETKGYDIAGTGTIDVDGKVGPIGGIDQKVVAADKAGKDIFFAPNQ</entry><entry>296</entry></row><row><entry /></row><row><entry>Query:</entry><entry>298</entry><entry>PVDKEIKKVNPNAISNYEEAKRAAKRLKTKMKIVPVTTVQEALVYLRK</entry><entry>345</entry></row><row><entry /><entry /><entry>         N  + S+Y+ A + AK + + MKIVPV T+Q+A+ YL K</entry></row><row><entry>Sbjct:</entry><entry>297</entry><entry>---------NGASNSDYKNAVKTAKDIDSNMKIVPVDTMQDAIDYLNK</entry><entry>335</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00157" num="00157"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 229/339 (67%), Positives = 276/339 (80%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>LKWWIIGFAFLLLVLASLVVRLPYYLEMPGGAYDIRSVLKVNKKADKAKGSYNFVAVSVS</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>+KWW++G   L+ +L +L   LPYY+EMPGGAYDIR+VL+VN K DK KG+Y FVAV +S</entry></row><row><entry>Sbjct:</entry><entry>7</entry><entry>IKWWLVGLLALISLLLALFFPLPYYIEMPGGAYDIRTVLQVNGKEDKRKGAYQFVAVGIS</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>77</entry><entry>QATPAQVLYAWLTPFTELSSKEETTGGFSNDDYLRINQFYMETSQNESIYQALKLANKQV</entry><entry>136</entry></row><row><entry /><entry /><entry>+A+ AQ+LYAWLTPFTE+S+ E+TTGG+S+ D+LRINQFYMETSQN +IYQAL LA K V</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>RASLAQLLYAWLTPFTEISTAEDTTGGYSDADFLRINQFYMETSQNAAIYQALSLAGKPV</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>SLTYKGVYVLNLAKNSTFKDRLHLADTVTGVNGKSFKNSSQLIKYVAALHLGDKVKVQYT</entry><entry>196</entry></row><row><entry /><entry /><entry>+L YKGVYVL++   STFK  LHLADTVTGVNGK F +S++LI YV+ L LGD+V VQ+T</entry></row><row><entry>Sbjct:</entry><entry>127</entry><entry>TLDYKGVYVLDVNNESTFKGTLHLADTVTGVNGKQFTSSAELIDYVSHLKLGDEVTVQFT</entry><entry>186</entry></row><row><entry /></row><row><entry>Query:</entry><entry>197</entry><entry>SQGKKKESVGKVIKLSNGKNGIGIGLTDHTEVLSDVPVDFNTEGVGGPSAGLMFTLAIYD</entry><entry>256</entry></row><row><entry /><entry /><entry>S  K K+ VG++IKL NGKNGIGI LTDHT V S+  V F+T+GVGGPSAGLMFTL IYD</entry></row><row><entry>Sbjct:</entry><entry>187</entry><entry>SDNKPKKGVGRIIKLKNGKNGIGIALTDHTSVNSEDTVIFSTKGVGGPSAGLMFTLDIYD</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>257</entry><entry>QLVKEDLRKGRKIAGTGTIEQNGHVGDIGGAGLKVVSAAKKGMDIFFVPNNPIDKNAKKG</entry><entry>316</entry></row><row><entry /><entry /><entry>Q+ KEDLRKGR IAGTGTI ++G VGDIGGAGLKVV+AA+ G DIFFVPNNP+DK  KK</entry></row><row><entry>Sbjct:</entry><entry>247</entry><entry>QITKEDLRKGRTIAGTGTIGKDGEVGDIGGAGLKVVAAAEAGADIFFVPNNPVDKEIKKV</entry><entry>306</entry></row><row><entry /></row><row><entry>Query:</entry><entry>317</entry><entry>KTKVQTNYQEAKAAAKRLGTKMKIVPVQNVQQAIDYLKK</entry><entry>355</entry></row><row><entry /><entry /><entry>     +NY+EAK AAKRL TKMKIVPV  VQ+A+ YL+K</entry></row><row><entry>Sbjct:</entry><entry>307</entry><entry>NPNAISNYEEAKRAAKRLKTKMKIVPVTTVQEALVYLRK</entry><entry>345</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8479&gt; and protein &lt;SEQ ID 8480&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00158" num="00158"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: 8.26</entry></row><row><entry>GvH: Signal Score (−7.5): −4.04</entry></row><row><entry>     Possible site: 25</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry>ALOM program count: 1 value: −11.04 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="70pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.04</entry><entry>Transmembrane</entry><entry>20-36 (12-43)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 4.51</entry><entry>70</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.71</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.5416(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00009" num="00009"><img id="EMI-C00009" he="103.72mm" wi="118.79mm" file="US07939087-20110510-C00009.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00009" attachment-type="cdx" file="US07939087-20110510-C00009.CDX" /><attachment idref="CHEM-US-00009" attachment-type="mol" file="US07939087-20110510-C00009.MOL" /></attachments></chemistry>

SEQ ID 8480 (GBS39) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 12</figref> (lane 9; MW 65.2 kDa) and <figref idrefs="DRAWINGS">FIG. 15</figref> (lane 3; MW 40 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 45

A DNA sequence (GBSx0044) was identified in <i>S. agalactiae </i>&lt;SEQ ID 143&gt; which encodes the amino acid sequence &lt;SEQ ID 144&gt;. This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00159" num="00159"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3908(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00160" num="00160"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB15227 GB:Z99120 similar to hypothetical proteins [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 114/280 (40%), Positives = 173/280 (61%), Gaps = 9/280 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTELIRILHLNDLHSHFENFPKVKRFFH----DNQAQPIETISLDLGDNIDKSHPLTEAS</entry><entry>56</entry><entry /></row><row><entry /><entry /><entry>M E +R+ H NDLHSHFEN+PK+  +      ++Q+   ET+  D+GD++D+   +TEA+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKEKLRLYHTNDLHSHFENWPKIVDYIEQKRKEHQSDGEETLVFDIGDHLDRFQFVTEAT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>57</entry><entry>SGKANVQLMNELGIELATIGNNEGVGLSKKDLDQVYKDSDFTVIVGNLKD-NIIEPSWAK</entry><entry>115</entry></row><row><entry /><entry /><entry> GKANV L+N L I+ A IGNNEG+ L  ++L  +Y  ++F VIV NL D N PSWA</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FGKANVDLLNRLHIDGAAIGNNEGITLPHEELAALYDNAEFPVIVSNLFDKNGNRPSWAV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>116</entry><entry>PYIIYETQQGTKLAFLAYTFPYYKTYEPNGWTIEDPIDCLKCHLQINEIK-EANCRILMS</entry><entry>174</entry></row><row><entry /><entry /><entry>PY I   + G  +AFL  T PYY  Y+  GWT+ D ++ +K    I E+K +A+  +L+S</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PYHIKSLKNGMSIAFLGVTVPYYPVYDKLGWTVTDALESIK--ETILEVKGQADIIVLLS</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>175</entry><entry>HLGIRFDTRIAQEFSEIDLIIGAHTHHLFEEGELINGTYLAAAGKYGRFVGSIDITFDNH</entry><entry>234</entry></row><row><entry /><entry /><entry>HLGI D  +A+   EID+I+ +HTHHL E+G+++NG  LA+A KYG +VG ++IT D+</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>HLGILDDQAVAEAVPEIDVILESHTHHLLEDGQVVNGVLLASAEKYGHYVGCVEITVDS-</entry><entry>237</entry></row><row><entry /></row><row><entry>Query:</entry><entry>235</entry><entry>TLKDILISTCDTKQLTGYPSDSDWLRRLSQKVKNSLEKKV</entry><entry>274</entry></row><row><entry /><entry /><entry>  + I   T   + +  +  +S   +    + +   E+K+</entry></row><row><entry>Sbjct:</entry><entry>238</entry><entry>VQRSINSKTASVQNMAEWTGESAETKAFLNEKEREAEEKL</entry><entry>277</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 46

A DNA sequence (GBSx0045) was identified in <i>S. agalactiae </i>&lt;SEQ ID 145&gt; which encodes the amino acid sequence &lt;SEQ ID 146&gt;. This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00161" num="00161"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="28pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.48</entry><entry>Transmembrane</entry><entry>5-21 (5-21)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1192(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9605&gt; which encodes amino acid sequence &lt;SEQ ID 9606&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00162" num="00162"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB15227 GB: Z99120 similar to hypothetical proteins [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 29/137 (21%), Positives = 71/137 (51%), Gaps = 13/137 (9%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>AMLFYAGADVAIINSGLIVQPFEKD-FSRKNLHESLPHQMRLAKLTVSSQELLEIYETIY</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>A+  +   D++++NSG+I+ P +    ++ +LH   PH +    + ++ +EL E    ++</entry></row><row><entry>Sbjct:</entry><entry>305</entry><entry>ALKEWCETDISMVNSGVILGPLKAGPVTKLDLHRICPHPINPVAVRLTGEELKETI--VH</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>QQGQFLAQQKIHGMGFRGKCFGEVLHSGFDYKN----------GKIVYNEKDIDAKEEVI</entry><entry>111</entry></row><row><entry /><entry /><entry>   + + Q +I G+GFRG+  G+++++G + +            +I  N +DI+  ++</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>AASEQMEQLRIKGLGFRGEVMGKMVYAGVEVETKRLDDGITHVTRITLNGEDIEKHKQYS</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>112</entry><entry>LVIVDQYYFASYFECLK</entry><entry>128</entry></row><row><entry /><entry /><entry>+ ++D +     F  ++</entry></row><row><entry>Sbjct:</entry><entry>423</entry><entry>VAVLDMFTLGKLFPLIR</entry><entry>439</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 47

A DNA sequence (GBSx0046) was identified in <i>S. agalactiae </i>&lt;SEQ ID 147&gt; which encodes the amino acid sequence &lt;SEQ ID 148&gt;. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00163" num="00163"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3567(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein differs from AX026665 at the C-terminus:

<tables id="TABLE-US-00164" num="00164"><table frame="none" colsep="0" rowsep="0" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="28pt" align="left" /><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="56pt" align="center" /><colspec colname="3" colwidth="49pt" align="left" /><colspec colname="4" colwidth="56pt" align="center" /><colspec colname="5" colwidth="0pt" align="left" /><tbody valign="top"><row><entry /><entry>Query:</entry><entry>181</entry><entry>SAKQHFVIRKK</entry><entry>191</entry><entry /></row><row><entry /><entry /><entry /><entry>SAKQH +  +K</entry></row><row><entry /><entry>Sbjct:</entry><entry>181</entry><entry>SAKQHLLFVRK</entry><entry>191</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 149&gt; which encodes the amino acid sequence &lt;SEQ ID 150&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00165" num="00165"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3974(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00166" num="00166"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 110/205 (53%), Positives = 147/205 (71%), Gaps = 15/205 (7%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MRKEVTPEMLNYNKYPGPQFIHFENIVKSDDIEFQLVINEKSAFDVTVFGQRFSEILLKY</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+KE++PEM NYNK+PGP+FIHFE  VK++ I+  L+ + K+AFD T FGQR++E+LLKY</entry><entry /></row><row><entry>Sbjct:</entry><entry>9</entry><entry>MKKEISPEMYNYNKFPGPKFIHFEEQVKAEGIDLLLLEDVKNAFDTTSFGQRYTEVLLKY</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>DFIVGDWGNEQLRLRGFYKDASTIRKNSRISRLEDYIKEYCNFGCAYFVLENPNPRDIKF</entry><entry>120</entry></row><row><entry /><entry /><entry>D+IVGDWGNEQLRL+GFYKD+  I+K +RISRLEDYIKE+CNFGCAYFVLEN +P+DIKF</entry><entry /></row><row><entry>Sbjct:</entry><entry>69</entry><entry>DYIVGDWGNEQLRLKGFYKDSDDIKKTNRISRLEDYIKEFCNFGCAYFVLENLHPQDIKF</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DDERPHKRRKS------RSKSQSSKSQTRNNRSQSNA--------NAHFTSKKRKDTKRR</entry><entry>166</entry></row><row><entry /><entry /><entry>++ER  +R+KS      R K   S  Q    +S+S          N  FTS+KR+   +</entry><entry /></row><row><entry>Sbjct:</entry><entry>129</entry><entry>EEERQPRRKKSPKSKSNRRKPNYSNQQPATPKSKSKRASKEKQPENQAFTSQKRRSNTKH</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>167</entry><entry>QERHIKEEQDKEMTSAKQHFVIRKK</entry><entry>191</entry></row><row><entry /><entry /><entry>+E+  K  Q  ++ +   HF+IRKK</entry><entry /></row><row><entry>Sbjct:</entry><entry>189</entry><entry>KEKS-KRNQTSQLNTKISHFIIRKK</entry><entry>212</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 48

A DNA sequence (GBSx0047) was identified in <i>S. agalactiae </i>&lt;SEQ ID 151&gt; which encodes the amino acid sequence &lt;SEQ ID 152&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00167" num="00167"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3627(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9607&gt; which encodes amino acid sequence &lt;SEQ ID 9608&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00168" num="00168"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06225 GB: AP001515 unknown conserved protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 205/349 (58%), Positives = 258/349 (73%), Gaps = 5/349 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>18</entry><entry>PSIYSLTRDELIAWAIEHGEKKFRASQIWDWLYKKRVQSFDEMTNISKDFIALLNENFVV</entry><entry>77</entry><entry /></row><row><entry /><entry /><entry>PSIY+L  +EL  W  E GE KFRA+QI++WLY+KRV+ F EMTN+SKD  A L ++F +</entry><entry /></row><row><entry>Sbjct:</entry><entry>17</entry><entry>PSIYTLQFEELEMWLKEQGEPKFRATQIFEWLYEKRVKQFQEMTNLSKDLRAKLEKHFNL</entry><entry>76</entry></row><row><entry /></row><row><entry>Query:</entry><entry>78</entry><entry>NPLKQRIVQESADGTVKYLFELPDGMLIETVLMRQHYGLSVCVTTQVGCNIGCTFCASGL</entry><entry>137</entry></row><row><entry /><entry /><entry>  LK    Q+S+DGT+K+LFEL DG  IETV+MR +YG SVCVTTQVGC +GCTFCAS L</entry><entry /></row><row><entry>Sbjct:</entry><entry>77</entry><entry>TTLKTVTKQQSSDGTIKFLFELHDGYSIETVVMRHNYGNSVCVTTQVGCRLGCTFCASTL</entry><entry>136</entry></row><row><entry /></row><row><entry>Query:</entry><entry>138</entry><entry>IKKQRDLNNGEITAQIMLVQKYFDERGQGERVSHIVVMGIGEPFDNYTNVLKFLRTVNDD</entry><entry>197</entry></row><row><entry /><entry /><entry>   +R+L  GEI AQ++  Q+  DE  QGERV  IVVMGIGEPFDNY  ++ FL+TVN D</entry><entry /></row><row><entry>Sbjct:</entry><entry>137</entry><entry>GGLKRNLEAGEIVAQVVEAQRAMDE--QGERVGSIVVMGIGEPFDNYQALMPFLKTVNHD</entry><entry>194</entry></row><row><entry /></row><row><entry>Query:</entry><entry>198</entry><entry>NGLAIGARHITVSTSGLAHKIREFANEGVQVNLAVSLHAPNNDLRSSIMRINRSFPLEKL</entry><entry>257</entry></row><row><entry /><entry /><entry> GL IGARHITVSTSG+  KI +FA+EG+Q+N A+SLHAPN +LRS +M +NR++PL KL</entry><entry /></row><row><entry>Sbjct:</entry><entry>195</entry><entry>KGLNIGARHITVSTSGVVPKIYQFADEGLQINFAISLHAPNTELRSKLMPVNRAWPLPKL</entry><entry>254</entry></row><row><entry /></row><row><entry>Query:</entry><entry>258</entry><entry>FAAIEYYIETTNRRVTFEYIMLNGVNDTPENAQELADLTKKIRKLSYVNLIPYNPVSEHD</entry><entry>317</entry></row><row><entry /><entry /><entry>  AI YYI+ T RRVTFEY +  G ND  E+A+ELADL K I+   +VNLIP N V E D</entry><entry /></row><row><entry>Sbjct:</entry><entry>255</entry><entry>MDAIRYYIDKTGRRVTFEYGLFGGENDQVEHAEELADLIKDIK--CHVNLIPVNYVPERD</entry><entry>312</entry></row><row><entry /></row><row><entry>Query:</entry><entry>318</entry><entry>QYSRSPKERVEAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSNTMKRD</entry><entry>366</entry></row><row><entry /><entry /><entry> Y R+P++++ AF   LK+ GVN  +R+E G DIDAACGQLR+   K +</entry><entry /></row><row><entry>Sbjct:</entry><entry>313</entry><entry>-YVRTPRDQIFAFERTLKERGVNVTIRREQGHDIDAACGQLRAKERKEE</entry><entry>360</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 153&gt; which encodes the amino acid sequence &lt;SEQ ID 154&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00169" num="00169"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2320(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00170" num="00170"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 316/353 (89%), Positives = 339/353 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>KPSIYSLTRDELIAWAIEHGEKKFRASQIWDWLYKKRVQSFDEMTNISKDFIALLNENFV</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>KPSIYSLTRDELIAWA+E G+K+FRA+QIWDWLYKKRVQSF+EMTNISKDF+++LN++F</entry><entry /></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KPSIYSLTRDELIAWAVERGQKQFRATQIWDWLYKKRVQSFEEMTNISKDFVSILNDSFC</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>77</entry><entry>VNPLKQRIVQESADGTVKYLFELPDGMLIETVLMRQHYGLSVCVTTQVGCNIGCTFCASG</entry><entry>136</entry></row><row><entry /><entry /><entry>VNPLKQR+VQESADGTVKYLFELPDGMLIETVLMRQHYG SVCVTTQVGCNIGCTFCASG</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>VNPLKQRVVQESADGTVKYLFELPDGMLIETVLMRQHYGHSVCVTTQVGCNIGCTFCASG</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>LIKKQRDLNNGEITAQIMLVQKYFDERGQGERVSHIVVMGIGEPFDNYTNVLKFLRTVND</entry><entry>196</entry></row><row><entry /><entry /><entry>LIKKQRDLN+GEITAQIMLVQKYFD+R QGERVSH+VVMGIGEPFDNY NV+ FLR +ND</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>LIKKQRDLNSGEITAQIMLVQKYFDDRKQGERVSHVVVMGIGEPFDNYKNVMCFLRVIND</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>197</entry><entry>DNGLAIGARHITVSTSGLAHKIREFANEGVQVNLAVSLHAPNNDLRSSIMRINRSFPLEK</entry><entry>256</entry></row><row><entry /><entry /><entry>DNGLAIGARHITVSTSGLAHKIR+FANEGVQVNLAVSLHAPNNDLRSSIMR+NRSFPLEK</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>DNGLAIGARHITVSTSGLAHKIRDFANEGVQVNLAVSLHAPNNDLRSSIMRVNRSFPLEK</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>257</entry><entry>LFAAIEYYIETTNRRVTFEYIMLNGVNDTPENAQELADLTKKIRKLSYVNLIPYNPVSEH</entry><entry>316</entry></row><row><entry /><entry /><entry>LF+AIEYYIE TNRRVTFEYIMLN VND+ + AQELADLTK IRKLSYVNLIPYNPVSEH</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>LFSAIEYYIEKTNRRVTFEYIMLNEVNDSIKQAQELADLTKTIRKLSYVNLIPYNPVSEH</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>317</entry><entry>DQYSRSPKERVEAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSNTMKRDRQK</entry><entry>369</entry></row><row><entry /><entry /><entry>DQYSRSPKERV AFYDVLKKNGVNCVVRQEHGTDIDAACGQLRS TMK+DR+K</entry><entry /></row><row><entry>Sbjct:</entry><entry>302</entry><entry>DQYSRSPKERVLAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSKTMKKDREK</entry><entry>354</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 49

A DNA sequence (GBSx0048) was identified in <i>S. agalactiae </i>&lt;SEQ ID 155&gt; which encodes the amino acid sequence &lt;SEQ ID 156&gt;. This protein is predicted to be VanZF. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00171" num="00171"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.61</entry><entry>Transmembrane</entry><entry> 86-102 (77-106)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.60</entry><entry>Transmembrane</entry><entry>  19-35 (15-42)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.15</entry><entry>Transmembrane</entry><entry>113-129 (109-134)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4843(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00172" num="00172"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAF36806 GB:AF155139 VanZF [<i>Paenibacillus popilliae</i>]</entry><entry /></row><row><entry>Identities = 45/154 (29%), Positives = 68/154 (43%), Gaps = 36/154 (23%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>RRFVWMLVIIYCLIIVRMCFGPQIMIEGVSTPNVQRFGRIVAL-------LVPFNSFRSL</entry><entry>69</entry><entry /></row><row><entry /><entry /><entry>R F+W+ V ++ L +V M  G           NV   GR   L       L+PF+S</entry></row><row><entry>Sbjct:</entry><entry>36</entry><entry>RHFLWVYVFLFYLALVYMMTG---------IGNVWVVGRYETLIRVSEINLLPFSS----</entry><entry>82</entry></row><row><entry /></row><row><entry>Query:</entry><entry>70</entry><entry>DQLTSFKEIFWVIGQNVVNILLLFPLIIGLLSLKPSLRKYKSVILLAFLMSIFIECTQVV</entry><entry>129</entry></row><row><entry /><entry /><entry>+ +T++          ++NI+L  PL   L ++ P  R  K+     F  S+ IE TQ++</entry></row><row><entry>Sbjct:</entry><entry>83</entry><entry>EGVTTY----------ILNIILFMPLGFLLPTIWPQFRTIKNTACTGFFFSLAIELTQLL</entry><entry>132</entry></row><row><entry /></row><row><entry>Query:</entry><entry>130</entry><entry>LDILIDANRVFEIDDLWTNTLGGPFALWTYRNIK</entry><entry>163</entry></row><row><entry /><entry /><entry>       +R+ +IDDL  NTLG       YR  K</entry></row><row><entry>Sbjct:</entry><entry>133</entry><entry>------NHRITDIDDLLMNTLGAIIGYLLYRAFK</entry><entry>160</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 50

A DNA sequence (GBSx0049) was identified in <i>S. agalactiae </i>&lt;SEQ ID 157&gt; which encodes the amino acid sequence &lt;SEQ ID 158&gt;. This protein is predicted to be multidrug resistance-like ATP-binding protein mdl. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00173" num="00173"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.79</entry><entry>Transmembrane</entry><entry>  18-34 (17-36)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.15</entry><entry>Transmembrane</entry><entry>247-263 (242-268)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.81</entry><entry>Transmembrane</entry><entry>160-176 (158-176)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.71</entry><entry>Transmembrane</entry><entry>141-157 (134-158)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.12</entry><entry>Transmembrane</entry><entry>  56-72 (56-73)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.69</entry><entry>Transmembrane</entry><entry>278-294 (277-294)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3718(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00174" num="00174"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB06055 ABC transporter (ATP-binding protein) [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 284/575 (49%), Positives = 406/575 (70%), Gaps = 2/575 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSIIKNLWWFFKEEKKRYLIGILSLSLVAVLNLIPPKIMGSVIDAITTGKLTRPQLLWNL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M +  +LWWFFK+EKK Y  GI+ L++V++L L+PP+++G ++D I  G LT P LL  +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKVFVDLWWFFKQEKKSYGFGIVMLAIVSLLTLVPPRVVGIIVDHIYEGTLTMPVLLQWI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LGLVLSALAMYGLRYIWRMYILGTSYKLGQVVRYRLFEHFTKMSPSFYQKYRTGDLMAHA</entry><entry>120</entry></row><row><entry /><entry /><entry>  L   AL +Y  RY+WR+ I G S +L +++R +L+ HFT M+  FYQK+RTGDLMAHA</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GVLAALALIVYVARYLWRVMIFGASLRLARLLRNQLYTHFTNMAAPFYQKHRTGDLMAHA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TNDINSLTRLAGGGVMSAVDASITALVTLITMFFTISWQMTLIAVIPLPLMALATSKLGR</entry><entry>180</entry></row><row><entry /><entry /><entry>TNDI ++   AG GV++ VD+       ++TM  TISW++TLI+++P+PLMAL TS  G</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TNDIRAIQATAGQGVLTLVDSLTMGGFVILTMAITISWELTLISLLPMPLMALLTSYYGS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KTHETFKESQAAFSELNNKVQESVSGVKVTKSFGYQEQEIASFQEVNQMTFVKNMRTMTY</entry><entry>240</entry></row><row><entry /><entry /><entry>  H+ F  +QAAFS LN+KVQESV+GV+VTK+FG +EQ+I +F++ +     KN+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LLHKRFHHAQAAFSSLNDKVQESVTGVRVTKAFGQEEQDIEAFRKQSDDVVKKNVAVARV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>DVMFDPLVLLFIGASYVLTLAMGAFMISKGQVTVGDLVTFVTYLDMLVWPLMAIGFLFNM</entry><entry>300</entry></row><row><entry /><entry /><entry>D +FDP + L +G SY L +  GA  +   Q+T+G L +F  YL +L+WP++A GFLFN+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>DALFDPTISLIVGLSYFLAIVFGARFVIAEQLTIGQLTSFTIYLGLLIWPMLAFGFLFNI</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>VQRGSVSYNRINSLLEQESDITDPLNPIRPVVNGTLRYDIDFFRYDN--EETLADIHFTL</entry><entry>358</entry></row><row><entry /><entry /><entry>V+RG  SYNR++ LL+ + +ITD    I     G +   ID F Y N  E  LAD+ F L</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>VERGRASYNRVSQLLQAKQEITDSRARIHVPPTGHVDVAIDQFVYPNQKEPALADVQFEL</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>359</entry><entry>EKGQTLGLVGQTGSGKTSLIKLLLREHDVTQGKITLNKHDIRDYRLSELRQLIGYVPQDQ</entry><entry>418</entry></row><row><entry /><entry /><entry> +G+TLG+VG+TG+GKT+L++LL RE+D+ QG I L+   I  Y L  L+   G VPQD</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>SEGETLGIVGKTGAGKTTLLRLLQREYDIKQGTIILDGRPIEHYTLDALKAAFGTVPQDH</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>419</entry><entry>FLFATSILENVRFGNPTLSINAVKKATKLAHVYDDIKQMPAGFETLIGEKGVSLSGGQKQ</entry><entry>478</entry></row><row><entry /><entry /><entry>FLF+ +I +N+ F  P  +I+ + + ++LAH++DDI Q   G++T++GE+GV+LSGGQKQ</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>FLFSATIADNIAFAKPDATISEIIQVSQLAHIHDDIIQFEQGYDTVVGERGVTLSGGQKQ</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>479</entry><entry>RIAMSRAMILDPDILILDDSLSAVDAKTEHAIIENLKTNRQGKSTIISAHRLSAVVHADL</entry><entry>538</entry></row><row><entry /><entry /><entry>R++++RA++ +P+ILILDDSLSAVDAKTE AI+ +L+  R+GK+TII+AHRLSA+ HAD</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>RVSIARALLANPNILILDDSLSAVDAKTEEAILSSLRAERKGKTTIITAHRLSAIKHADH</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>539</entry><entry>ILVMQDGRVIERGQHQELLNKGGWYAETYASQQLE</entry><entry>573</entry></row><row><entry /><entry /><entry>ILVM DGR++ERG H+ L+  GGWY   Y  QQLE</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>ILVMDDGRIVERGTHETLMEAGGWYRNMYERQQLE</entry><entry>575</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 8.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 159&gt; which encodes the amino acid sequence &lt;SEQ ID 160&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00175" num="00175"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.75</entry><entry>Transmembrane</entry><entry>176-192 (173-197)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.78</entry><entry>Transmembrane</entry><entry>267-283 (265-285)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.09</entry><entry>Transmembrane</entry><entry>  18-34 (15-40)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.13</entry><entry>Transmembrane</entry><entry>151-167 (150-169)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.69</entry><entry>Transmembrane</entry><entry> 85-101 (85-101)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4100(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00176" num="00176"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 172/609 (28%), Positives = 315/609 (51%), Gaps = 58/609 (9%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSIIKNLWWFFKEEKKRYLIGILSLSLVAVLNLIPPKIMGSVIDAITTGKLTRPQLLWNL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M   +  W++FK  +  + +  +++ L   L +  P  +G  +  +  GK+ +   +  +</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>MKTARFFWFYFKRYRFSFTVIAVAVILATYLQVKAPVFLGESLTEL--GKIGQAYYVAKM</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LGLV-----LSAL--AMYGLRYIWRMYILGT---SYKLGQVV-------RYRLFEHFTKM</entry><entry>103</entry></row><row><entry /><entry /><entry> G       LSA    M+ L   +   +L     S+ L +VV       R  LF    ++</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>SGQTHFSPDLSAFNAVMFKLLMTYFFTVLANLIYSFLLTRVVSHSTNRMRKGLFGKLERL</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>104</entry><entry>SPSFYQKYRTGDLMAHATNDINSLTRLAGGGVMSAVDASITALVTLITMFFTISWQM---</entry><entry>160</entry></row><row><entry /><entry /><entry>+ +F+ +++ G++++  T+D+++        + ++++ S+  +VT I ++  + W M</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>TVAFFDRHKDGEILSRFTSDLDN--------IQNSLNQSLIQVVTNIALYIGLVWMMFRQ</entry><entry>171</entry></row><row><entry /></row><row><entry>Query:</entry><entry>161</entry><entry>------TLIAVIPLPLMALATS-KLGRKTHETFKESQAAFSELNNKVQESVSGVKVTKSF</entry><entry>213</entry></row><row><entry /><entry /><entry>        IA  P+ L+ L  + +L RK        Q   S LN  + E++SG K</entry></row><row><entry>Sbjct:</entry><entry>172</entry><entry>DSRLALLTIASTPVALIFLVINIRLARKYTNI---QQQEVSALNAFMDETISGQKAIIVQ</entry><entry>228</entry></row><row><entry /></row><row><entry>Query:</entry><entry>214</entry><entry>GYQEQEIASF----QEVNQMTFVKNMRT------MTYDVMFDPLVLLFIGASYVLT-LAM</entry><entry>262</entry></row><row><entry /><entry /><entry>G QE  + +F    + V Q TF + + +      M    + +  +++F+G++ VL+  +M</entry></row><row><entry>Sbjct:</entry><entry>229</entry><entry>GVQEDTMTAFLKHNERVRQATFKRRLFSGQLFPVMNGMSLINTAIVIFVGSTIVLSDKSM</entry><entry>288</entry></row><row><entry /></row><row><entry>Query:</entry><entry>263</entry><entry>GAFMISKGQVTVGDLVTFVTYLDMLVWPLMAIGFLFNMVQRGSVSYNRINSLLEQESDIT</entry><entry>322</entry></row><row><entry /><entry /><entry> A         +G +VTFV Y      P+M I   +  +Q      +RI  + ++  ++</entry></row><row><entry>Sbjct:</entry><entry>289</entry><entry>PA------AAALGLVVTFVQYSQQYYQPMMQIASSWGELQLAFTGAHRIQEMFDETEEVR</entry><entry>342</entry></row><row><entry /></row><row><entry>Query:</entry><entry>323</entry><entry>DPLNPIRPVVNGTLRYD-IDFFRYDNEETLADIHFTLEKGQTLGLVGQTGSGKTSLIKLL</entry><entry>381</entry></row><row><entry /><entry /><entry>    P    +   +  + +DF     ++ L+D+     KG+ + +VG TGSGKT+++ L+</entry></row><row><entry>Sbjct:</entry><entry>343</entry><entry>PQNAPAFTSLKEAVAINHVDFGYLPGQKVLSDVSIVAPKGKMIAVVGPTGSGKTTIMNLI</entry><entry>402</entry></row><row><entry /></row><row><entry>Query:</entry><entry>382</entry><entry>LREHDVTQGKITLHKHDIRDYRLSELRQLIGYVPQDQFLFATSILENVRFGNPTLSINAV</entry><entry>441</entry></row><row><entry /><entry /><entry> R +DV  G IT +  DIRDY L  LRQ +G V Q+  LF+ +I +N+RFG+ T+S + V</entry></row><row><entry>Sbjct:</entry><entry>403</entry><entry>NRFYDVDAGSITFDGRDIRDYDLDSLRQKVGIVLQESVLFSGTITDNIRFGDQTISQDMV</entry><entry>462</entry></row><row><entry /></row><row><entry>Query:</entry><entry>442</entry><entry>KKATKLAHVYDDIKQMPAGFETLIGEKGVSLSGGQKQRIAMSRAMILDPDILILDDSLSA</entry><entry>501</entry></row><row><entry /><entry /><entry>+ A +  H++D I  +P G+ T + +     S GQKQ I+++R ++ DP++LILD++ S</entry></row><row><entry>Sbjct:</entry><entry>463</entry><entry>ETAARATHIHDFIMSLPKGYNTYVSDDDNVFSTGQKQLISIARTLLTDPEVLILDEATSN</entry><entry>522</entry></row><row><entry /></row><row><entry>Query:</entry><entry>502</entry><entry>VDAKTEHAIIENLKTNRQGKSTIISAHRLSAVVHADLILVMQDGRVIERGQHQELLNKGG</entry><entry>561</entry></row><row><entry /><entry /><entry>VD  TE  I   ++    G+++ + AHRL  +++AD I+V++DG+VIE+G H ELL++ G</entry></row><row><entry>Sbjct:</entry><entry>523</entry><entry>VDTVTESKIQRAMEAIVAGRTSFVIAHRLKTILNADHIIVLKDGKVIEQGNHHELLHQKG</entry><entry>582</entry></row><row><entry /></row><row><entry>Query:</entry><entry>562</entry><entry>WYAETYASQ</entry><entry>570</entry></row><row><entry /><entry /><entry>+YAE Y +Q</entry></row><row><entry>Sbjct:</entry><entry>583</entry><entry>FYAELYHNQ</entry><entry>591</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 51

A DNA sequence (GBSx0050) was identified in <i>S. agalactiae </i>&lt;SEQ ID 161&gt; which encodes the amino acid sequence &lt;SEQ ID 162&gt;. This protein is predicted to be mdlB (ATP-bindingprot). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00177" num="00177"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.65</entry><entry>Transmembrane</entry><entry>164-180 (155-183)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.15</entry><entry>Transmembrane</entry><entry>  25-41 (21-46)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.88</entry><entry>Transmembrane</entry><entry>143-159 (133-163)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.49</entry><entry>Transmembrane</entry><entry>251-267 (251-270)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>  61-77 (61-77)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4461(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00178" num="00178"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB06054 ABC transporter (ATP-binding protein) [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 278/582 (47%), Positives = 398/582 (67%), Gaps = 6/582 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MMKSNQWQVFKRLISYLRPYKWFTVLALSLLLLTTVVKNIIPLIASHFIDHYLT-NVNQT</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>+    Q  VFKRL+SY   YK   ++A  LL + T  + +P+I   FID YLT     T</entry><entry /></row><row><entry>Sbjct:</entry><entry>9</entry><entry>LSSKEQRTVFKRLLSYAAHYKGQLMVAFLLLFIATGAQLLGPIIVKIFIDDYLTPRYFPT</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>AVLILVG--YYSMYVLQTLIQYFGNLFFARVSYSIVRDIRRDAFANMERLGMSYFDRTPA</entry><entry>117</entry></row><row><entry /><entry /><entry> VL L+G  Y  +++   +I Y+    F +V+ SIV+ +R D F++++RLG+S+FD+TPA</entry><entry /></row><row><entry>Sbjct:</entry><entry>69</entry><entry>DVLFLLGAGYLVLHLTAVIIDYYQLFLFQKVALSIVQRLRIDVFSSVQRLGLSFFDQTPA</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>GSIVSRITNDTEAISDMFSGILSSFISAIFIFTVTLYTMLMLDIKLTGLVALLLPVIFIL</entry><entry>177</entry></row><row><entry /><entry /><entry>G +VSRITNDTE+I +++  +L++F+  I         M  L++ L     +LLP+IF L</entry><entry /></row><row><entry>Sbjct:</entry><entry>129</entry><entry>GGLVSRITNDTESIKELYVTVLATFVQNIIFLIGIFAAMFYLNVTLAIYCLVLLPLIFAL</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>VNVYRKKSVTVIAKTRSLLSDINSKLSESIEGIRIVQAFGQEERLKTEFEEINKEHVVYA</entry><entry>237</entry></row><row><entry /><entry /><entry>+ VYRK S    A     LS +N +++ESI+G+ I+Q F QE R++ EF  IN EH +</entry><entry /></row><row><entry>Sbjct:</entry><entry>189</entry><entry>MQVYRKYSSRFYADMSEKLSLLNGRINESIQGMAIIQMFRQERRMRKEFSAINDEHFLAG</entry><entry>248</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>NRSMALDSLFLRPAMSLLKLLAYAVLMAYFGFTGVKGGLTAGLMYAFIQYVNRLFDPLIE</entry><entry>297</entry></row><row><entry /><entry /><entry> +SM LD L LRPA+ +L +LA  ++++YFG   +   +  G++YAF+ Y++R F+P+ +</entry><entry /></row><row><entry>Sbjct:</entry><entry>249</entry><entry>MKSMKLDGLLLRPAVDVLSILALMLILSYFGIMSMDTAVEIGVVYAFVNYLDRFFEPVNQ</entry><entry>308</entry></row><row><entry /></row><row><entry>Query:</entry><entry>298</entry><entry>VTQNFSTLQTSMVSAGRVFDLIDETGFEPSQKNTE--AFVREGNIEFKNVSFSYDGKKQI</entry><entry>355</entry></row><row><entry /><entry /><entry>+    S  Q ++VSAGRVF L+D     P ++  E  A + EGN+EF+NVSFSYDGK  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>309</entry><entry>MMMRLSMFQQAIVSAGRVFKLMDHRELAPDREGNEHPAIIGEGNVEFRNVSFSYDGKTNV</entry><entry>368</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>LDNVSFSVKKGETIAFVGATGSGKSSIINVFMRFYEFQSGQVLLDGKDIRDYSQEQLRKN</entry><entry>415</entry></row><row><entry /><entry /><entry>L N+SF+VKKGET+A VG TGSGK+SIINV MRFY  Q G++L+DGK +  +   +LR</entry><entry /></row><row><entry>Sbjct:</entry><entry>369</entry><entry>LKNISFTVKKGETVALVGHTGSGKTSIINVLMRFYPLQDGEILIDGKPLTSFENNELRAK</entry><entry>428</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>IGLVLQDPFLYHGTIKSNIKMY-QDITDQEVQDAAEFVDADQFIQKLPDKYDAAVSERGS</entry><entry>474</entry></row><row><entry /><entry /><entry>+GLVLQDPFLY GTI SNI++Y Q I+D  ++ AA FV AD FI++L   Y+  V+ERG+</entry><entry /></row><row><entry>Sbjct:</entry><entry>429</entry><entry>VGLVLQDPFLYTGTIASNIRLYDQAISDDRIKRAASFVRADGFIERLSHGYETKVTERGA</entry><entry>488</entry></row><row><entry /></row><row><entry>Query:</entry><entry>475</entry><entry>SFSTGQRQLLAFARTVASKPKILILDEATANIDSETEQIVQDSLAKMRQGRTTIAIAHRL</entry><entry>534</entry></row><row><entry /><entry /><entry>+FS+GQRQLL+FART+  +P ILILDEATA++D+ETE+ +Q++L +M+QGRTTIAIAHRL</entry><entry /></row><row><entry>Sbjct:</entry><entry>489</entry><entry>TFSSGQRQLLSFARTMVREPAILILDEATASVDTETEEAIQEALERMKQGRTTIAIAHRL</entry><entry>548</entry></row><row><entry /></row><row><entry>Query:</entry><entry>535</entry><entry>STIQDANCIYVLDRGKIIESGNHESLLDLKGTYYRMYQLQAG</entry><entry>576</entry></row><row><entry /><entry /><entry>STI+DA+ I VL +G+I+E G H+ L+  KG Y +MY LQ G</entry><entry /></row><row><entry>Sbjct:</entry><entry>549</entry><entry>STIKDADQILVLHQGEIVERGTHDELIAKKGLYQKMYVLQKG</entry><entry>590</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 160.

A related GBS gene &lt;SEQ ID 8481&gt; and protein &lt;SEQ ID 8482&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00179" num="00179"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: −4.63</entry></row><row><entry>GvH: Signal Score (−7.5): −5.85</entry></row><row><entry>Possible site: 39</entry></row><row><entry>&gt;&gt;&gt;Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="91pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="126pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program count: 5</entry><entry>value: −8.65</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="center" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −8.65</entry><entry>Transmembrane</entry><entry>164-180 (155-183)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.15</entry><entry>Transmembrane</entry><entry>25-41 (21-46)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.88</entry><entry>Transmembrane</entry><entry>143-159 (133-163)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.49</entry><entry>Transmembrane</entry><entry>251-267 (251-270)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>61-77 (61-77)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 3.02</entry><entry>483</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.23</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial membrane --- Certainty =0.4461 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty =0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty =0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00010" num="00010"><img id="EMI-C00010" he="156.55mm" wi="120.14mm" file="US07939087-20110510-C00010.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00010" attachment-type="cdx" file="US07939087-20110510-C00010.CDX" /><attachment idref="CHEM-US-00010" attachment-type="mol" file="US07939087-20110510-C00010.MOL" /></attachments></chemistry>

There is also homology to SEQ IDs 330, 4634 and 5788.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 52

A DNA sequence (GBSx0051) was identified in <i>S. agalactiae </i>&lt;SEQ ID 163&gt; which encodes the amino acid sequence &lt;SEQ ID 164&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00180" num="00180"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0635(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9609&gt; which encodes amino acid sequence &lt;SEQ ID 9610&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00181" num="00181"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAA25224 GB: M87483 anthranilate synthase beta subunit</entry><entry /></row><row><entry>[<i>Lactococcus lactis</i>]</entry></row><row><entry>Identities = 101/191 (52%), Positives = 133/191 (68%), Gaps = 4/191 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>14</entry><entry>MLLLVDNYDSFTYNLKQYLSVYKEVFVIKNDVPNLFLLAESAEAIVLSPGPGHPKDAGKM</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>M+L++DNYDSFTYNL QY+ V  +V V+KND  +L  +AE A+A++ SPGPG P DAGKM</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MILIIDNYDSFTYNLVQYVGVLTDVAVVKNDDDSLGNMAEKADALIFSPGPGWPADAGKM</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>VELINQFIGKKPILGICLGHQALAECLGGRLNLANHVMHGKQSWVTINDHTSLFKGIDSP</entry><entry>133</entry></row><row><entry /><entry /><entry>  LI QF G+KPILGICLG QA+ E  GG+L LA+ VMHGK S V       +F  + S</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ETLIQQFAGQKPILGICLGFQAIVEVFGGKLRLAHQVMHGKNSQVRQTSGNLIFNHLPSK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>134</entry><entry>TQVMRYHSLVVTD---LPENIAVIARSNEDNEIMAFHCPSLKVYAMQFHPESIGSIDGMK</entry><entry>190</entry></row><row><entry /><entry /><entry>  VMRYHS+V+ +   LP+  A+ A + +D EIMA      ++Y +QFHPESIG++DGM</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>FLVMRYHSIVMDEAVALPD-FAITAVATDDGEIMAIENEKEQIYGLQFHPESIGTLDGMT</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>191</entry><entry>MIENFLTLIND</entry><entry>201</entry></row><row><entry /><entry /><entry>MIENF+  +N+</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>MIENFVNQVNE</entry><entry>190</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 165&gt; which encodes the amino acid sequence &lt;SEQ ID 166&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00182" num="00182"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3183(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00183" num="00183"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 104/186 (55%), Positives = 131/186 (69%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>14</entry><entry>MLLLVDNYDSFTYNLKQYLSVYKEVFVIKNDVPNLFLLAESAEAIVLSPGPGHPKDAGKM</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>M+LL+DNYDSFTYNL QYLS + E  V+ N  PNL+ +A+ A A+VLSPGPG PK+A +M</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MILLIDNYDSFTYNLAQYLSEFDETIVLYNQDPNLYDMAKKANALVLSPGPGWPKEANQM</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>VELINQFIGKKPILGICLGHQALAECLGGRLNLANHVMHGKQSWVTINDHTSLFKGIDSP</entry><entry>133</entry></row><row><entry /><entry /><entry> +LI  F   KPILG+CLGHQA+AE LGG L LA  VMHG+QS +      SLF+ +</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PKLIQDFYQTKPILGVCLGHQAIAETLGGTLRLAKRVMHGRQSTIETQGPASLFRSLPQE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>134</entry><entry>TQVMRYHSLVVTDLPENIAVIARSNEDNEIMAFHCPSLKVYAMQFHPESIGSIDGMKMIE</entry><entry>193</entry></row><row><entry /><entry /><entry>  VMRYHS+VV  LP+  +V AR  +D EIMAF   +L ++ +QFHPESIG+ DGM MI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>ITVMRYHSIVVDQLPKGFSVTARDCDDQEIMAFEHHTLPLFGLQFHPESIGTPDGMTMIA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>194</entry><entry>NFLTLI</entry><entry>199</entry></row><row><entry /><entry /><entry>NF+  I</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>NFIAAI</entry><entry>186</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 53

A DNA sequence (GBSx0052) was identified in <i>S. agalactiae </i>&lt;SEQ ID 167&gt; which encodes the amino acid sequence &lt;SEQ ID 168&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00184" num="00184"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.17</entry><entry>Transmembrane</entry><entry>117-133 (108-140)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.70</entry><entry>Transmembrane</entry><entry>150-166 (150-166)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4270(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00185" num="00185"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB12877 GB: Z99109 similar to biotin biosynthesis [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 70/168 (41%), Positives = 106/168 (62%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>YIALMVALLIVLGFIPGIPLGFIPVPIVLQNLGVMLAGALLGSRKGFLAVAIFLLLVAIG</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>+IA+  AL+ VLGF+P + L F PVPI LQ LGVMLAG++L  +  FL+  +FLLLVA G</entry></row><row><entry>Sbjct:</entry><entry>9</entry><entry>HIAIFTALMAVLGFMPPLFLSFTPVPITLQTLGVMLAGSILRPKSAFLSQLVFLLLVAFG</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>APFLPGGRSGLVTLFGPTAGYLLTYPFAAFFIGLGLEKVKTTKLWVQFLIIWIFGVLLID</entry><entry>127</entry></row><row><entry /><entry /><entry>AP LPGGR G    FGP+AG+L+ YP A++ I L   +++   +   F    +FG++ I</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>APLLPGGRGGFGVFFGPSAGFLIAYPLASWLISLAANRLRKVTVLRLFFTHIVFGIIFIY</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>128</entry><entry>ICGSIVLSFQTSLPLTKSLFSNLIFIPGDTLKASICLIIYRKFANRLT</entry><entry>175</entry></row><row><entry /><entry /><entry>+ G  V +F   + L+++ F +L ++PGD +KA++   +  K    L+</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>LLGIPVQAFIMHIDLSQAAFMSLAYVPGDLIKAAVSAFLAIKITQALS</entry><entry>176</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 169&gt; which encodes the amino acid sequence &lt;SEQ ID 170&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00186" num="00186"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.03</entry><entry>Transmembrane</entry><entry>113-129 (109-139)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.97</entry><entry>Transmembrane</entry><entry>  55-71 (52-76)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.54</entry><entry>Transmembrane</entry><entry>  10-26 (6-38)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry> 86-102 (81-105)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.87</entry><entry>Transmembrane</entry><entry>  33-49 (28-51)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.97</entry><entry>Transmembrane</entry><entry>150-166 (150-168)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5012(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00187" num="00187"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 80/168 (47%), Positives = 108/168 (63%), Gaps = 1/168 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>TRTTTYIALMVALLIVLGFIPGIPLGFIPVPIVLQNLGVMLAGALLGSRKGFLAVAIFLL</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>T+    +A+M  L+I+LGFIP IPLGFIPVPIVLQNLGVMLAG +LG +KG L+V +F L</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>TKELVKVAMMTTLIIILGFIPAIPLGFIPVPIVLQNLGVMLAGLMLGGKKGTLSVFLF-L</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>LVAIGAPFLPGGRSGLVTLFGPTAGYLLTYPFAAFFIGLGLEKVKTTKLWVQFLIIWIFG</entry><entry>122</entry></row><row><entry /><entry /><entry>++ +  P   G R+ +  L GP+AGY++ Y        L      +    + FL + I G</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>VIGLFLPVFSGSRTTIPVLMGPSAGYVIAYLLVPIVFSLLYRNWFSKSTPLAFLALLISG</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>VLLIDICGSIVLSFQTSLPLTKSLFSNLIFIPGDTLKASICLIIYRKF</entry><entry>170</entry></row><row><entry /><entry /><entry>V+L+D+ G+I LS  T + L  SL SNL+FIPGDT+KA I  II  K+</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>VVLVDVLGAIWLSAYTGMSLVTSLLSNLVFIPGDTIKAIIATIIAVKY</entry><entry>170</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 54

A DNA sequence (GBSx0053) was identified in <i>S. agalactiae </i>&lt;SEQ ID 171&gt; which encodes the amino acid sequence &lt;SEQ ID 172&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00188" num="00188"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3914(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 55

A DNA sequence (GBSx0054) was identified in <i>S. agalactiae </i>&lt;SEQ ID 173&gt; which encodes the amino acid sequence &lt;SEQ ID 174&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00189" num="00189"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>             bacterial cytoplasm --- Certainty = 0.1864(Affirmative) &lt; succ&gt;</entry></row><row><entry>              bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9611&gt; which encodes amino acid sequence &lt;SEQ ID 9612&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00190" num="00190"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05467 GB: AP001513 biotin synthase [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 133/316 (42%), Positives = 201/316 (63%), Gaps = 2/316 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>NYIHLADEILSGKTSISYEQALEILNS-DENWWEIYAAALYLKNQVSRNNIRLNVLLSAK</entry><entry>75</entry><entry /></row><row><entry /><entry /><entry>N+I LA E++ GK  IS  +AL ILNS D+    +   A  ++       ++LN++++AK</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>NWIQLAQEVIEGKR-ISENEALAILNSPDDELLLLLQGAFTIRQTYYGKKVKLNMIMNAK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>76</entry><entry>QGLCAENCGYCSQSKESTADIDKFGLLPQNVILKQAIVAHQNGASVFCIAMSGTKPSKRE</entry><entry>135</entry></row><row><entry /><entry /><entry> G C ENCGYCSQS  S A ID + ++ +  IL+ A  AH+     +CI  SG  P+ R+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>SGFCPENCGYCSQSSISKAPIDAYPMVNKETILEGAKRAHELNVGTYCIVASGRGPTNRD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>136</entry><entry>IEQLCQVIPEIKKSLPLEICLTAGFLDREQLHQLKQAGIDRINHNLNTPEENYPNIATTH</entry><entry>195</entry></row><row><entry /><entry /><entry>I+ + + + EIK +  L+IC   G L  EQ  QLK AG+DR NHN+NT   ++  I T+H</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IDHVTEAVREIKDTYGLKICACLGILKPEQAEQLKAAGVDRYNHNVNTSARHHDQITTSH</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>196</entry><entry>SFKDRCDTLERIHNEDIDVCSGFICGMGESDEGLITLAFRLKELDPYSIPVNFLLAVEGT</entry><entry>255</entry></row><row><entry /><entry /><entry>+++DR +T+E + +  I  CSG I GM E+ E ++ +AF+L+ELD  SIPVNFL A++GT</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>TYEDRVNTVEVVKHSGISPCSGVIVGMKETKEDVVDMAFQLRELDADSIPVNFLHAIDGT</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>256</entry><entry>PLGKYNYLTPIKCLKIMAMLRFVFPFKELRLSAGREVHFENFESLVTLLVDSTFLGNYLT</entry><entry>315</entry></row><row><entry /><entry /><entry>PL   + LTPI CLK++++ R+V P KE+R+S GREV+ ++ + L     +S F+G+YLT</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>PLQGVHELTPIYCLKVLSLFRYVCPTKEIRISGGREVNLKSLQPLGLYAANSIFIGDYLT</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>316</entry><entry>EGGRNQHTDIEFLEKL</entry><entry>331</entry></row><row><entry /><entry /><entry>  G+ +  D + L+ L</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>TAGQEETADHQILKDL</entry><entry>316</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 56

A DNA sequence (GBSx0055) was identified in <i>S. agalactiae </i>&lt;SEQ ID 175&gt; which encodes the amino acid sequence &lt;SEQ ID 176&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00191" num="00191"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3440(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9613&gt; which encodes amino acid sequence &lt;SEQ ID 9614&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 57

A DNA sequence (GBSx0056) was identified in <i>S. agalactiae </i>&lt;SEQ ID 177&gt; which encodes the amino acid sequence &lt;SEQ ID 178&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00192" num="00192"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1985(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 58

A DNA sequence (GBSx0057) was identified in <i>S. agalactiae </i>&lt;SEQ ID 179&gt; which encodes the amino acid sequence &lt;SEQ ID 180&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00193" num="00193"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.11</entry><entry>Transmembrane</entry><entry>347-363 (347-363)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1044(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>             bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00194" num="00194"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAC11722 GB: AL445064 acetyl-CoA acetyltransferase related</entry><entry /></row><row><entry>protein [<i>Thermoplasma acidophilum</i>]</entry></row><row><entry>Identities = 113/388 (29%), Positives = 181/388 (46%), Gaps = 31/388 (7%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>RDVYIGFGLRTPIGIKGKQFKHYR-PELLGAHLLNQIKKIESESNID-----SIICGNTV</entry><entry>57</entry><entry /></row><row><entry /><entry /><entry>RDV+I    RT IG  G+ F   + P+L GA     IK +  E+++D      +I GN +</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>RDVFIVAAKRTAIGKFGRSFSKLKAPQLGGA----AIKAVMDEAHVDPASVEEVIMGNVI</entry><entry>57</entry></row><row><entry /></row><row><entry>Query:</entry><entry>58</entry><entry>--GTGGNIGRLMTLFSDYESYIPVQTIDMQCASSSSALFFGYLKISTGINEKVLVGGIES</entry><entry>115</entry></row><row><entry /><entry /><entry>  G G N            + +   T+++ CAS   A+     +I+ G  + V+ GG+ES</entry></row><row><entry>Sbjct:</entry><entry>58</entry><entry>QAGNGQNPAGQAAFHGGLPNSVLKYTVNVVCASGMLAVESAAREIALGERDLVIAGGMES</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>116</entry><entry>SSLQPMR-----RYAKEDNRNGEYTVAQ-FSPDSYAETVMLE----GAQRVCQKYGFRRE</entry><entry>165</entry></row><row><entry /><entry /><entry> S  P       R+  +   +  Y +      D   +    E     A+R  +K+G  RE</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>MSNAPFLLPADLRWGPKHLLHKNYKIDDAMLTDGLLDAFYFEHMGVSAERTSRKFGITRE</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>166</entry><entry>MLDKLAFLSHKRALTAKQGGYLEEVILPMEGM-RDQGVRKLKETFFQKLPRLMENSPLLT</entry><entry>224</entry></row><row><entry /><entry /><entry>M D+ +  S++RA+ A + G   + I+  EG+  D+G+RK       +LP   + + +LT</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>MADEYSVQSYERAIRATESGEFADEIVQFEGLDHDEGIRKTTMEDLARLPPAFDKNGILT</entry><entry>237</entry></row><row><entry /></row><row><entry>Query:</entry><entry>225</entry><entry>IGNVCLMHDAAAFLTLQSQKT--EFRIVHIVEVAG------DPKLSPELVHTATEKLLTE</entry><entry>276</entry></row><row><entry /><entry /><entry> GH   + D  + L + S+K   E+ +  I  + G      DP    E    AT KLL +</entry></row><row><entry>Sbjct:</entry><entry>238</entry><entry>AGNSAQLSDGGSALMIASEKAINEYGLKPIARITGYEQASLDPLDFVEAPIPATRKLLEK</entry><entry>297</entry></row><row><entry /></row><row><entry>Query:</entry><entry>277</entry><entry>THTKISDYDAIEWNEPFAAIDALFNHYYPEEREKFNIFGGTLAYGHPYACSGIINILHLM</entry><entry>336</entry></row><row><entry /><entry /><entry> H  I  YD +E NE F+    +  +    + E+FN+ GG +A GHP   SG   I+ LM</entry></row><row><entry>Sbjct:</entry><entry>298</entry><entry>QHKSIDYYDLVEHNEAFSIASVIVRNELKIDNERFNVNGGAVAIGHPIGNSGARIIVTLM</entry><entry>357</entry></row><row><entry /></row><row><entry>Query:</entry><entry>337</entry><entry>QALKYKNKPMGLTAIAGAGGVGMAISIE</entry><entry>364</entry></row><row><entry /><entry /><entry> ALK+++   GL  +   GG    +++E</entry></row><row><entry>Sbjct:</entry><entry>358</entry><entry>NALKHRHLKTGLATLCHGGGGAHTLTLE</entry><entry>385</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 181&gt; which encodes the amino acid sequence &lt;SEQ ID 182&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00195" num="00195"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.28</entry><entry>Transmembrane</entry><entry>345-361 (345-361)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1510(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00196" num="00196"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB03328 GB: AB035449 acetyl-CoA c-acetyltransferase</entry><entry /></row><row><entry>[<i>Staphylococcus aureus</i>]</entry></row><row><entry>Identities = 115/382 (30%), Positives = 184/382 (48%), Gaps = 29/382 (7%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTDVYIAAGLRTPIGLVGKQFAKEQPEILGAKLINALQNKYPV---PIDQVICGNTVGTG</entry><entry>57</entry><entry /></row><row><entry /><entry /><entry>M    I A  RT  G  G      +PE L   L    + KYP     ID V+ GN VG G</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNQAVIVAAKRTAFGKYGGTLKHLEPEQLLKPLFQHFKEKYPEVISKIDDVVLGNVVGNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>58</entry><entry>GNIGRLMTLYSHLGESVSALTVDMQCASAGAALSVGYAKIKAGMASNLLVGGIESSS---</entry><entry>114</entry></row><row><entry /><entry /><entry>GNI R   L + L +S+  +T+D QC S   ++      I+AG     + GG+ES+S</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GNIARKALLEAGLKDSIPGVTIDRQCGSGLESVQYACRMIQAGAGKVYIAGGVESTSRAP</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>115</entry><entry>---LQPESVYASADWRQGAYKVAQFSPDSISPFAMIEGAERVAREHGFTKEYLNHWTLRS</entry><entry>171</entry></row><row><entry /><entry /><entry>    +P SVY +A      Y+ A F+P+   P +MI+GAE VA+ +  ++E  + +  RS</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>WKIKRPHSVYETA--LPEFYERASFAPEMSDP-SMIQGAENVAKMYDVSRELQDEFAYRS</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>172</entry><entry>HQKASYCQEQALLADLILDLSGA-----SDQGIRPRLSSKVLSKVPPILGEGHVISAANA</entry><entry>226</entry></row><row><entry /><entry /><entry>HQ  +   +   ++  IL ++       +D+ ++  +      +  P++ +G  ++AAN+</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>HQLTAENVKNGNISQEILPITVKGEIFNTDESLKSHIPKDNFGRFKPVI-KGGTVTAANS</entry><entry>236</entry></row><row><entry /></row><row><entry>Query:</entry><entry>227</entry><entry>CLTHDAAAFLQLSSQPSAFKL--------IDVVEVAGDPQRSPLMVIKASQVLLEKHGLG</entry><entry>278</entry></row><row><entry /><entry /><entry>C+ +D A  L +  +  A++L         D V V  D     +  + A   LL+++ L</entry></row><row><entry>Sbjct:</entry><entry>237</entry><entry>CMKNDGAVLLLIMEKDMAYELGFEHGLLFKDGVTVGVDSNFPGIGPVPAISNLLKRNQLT</entry><entry>296</entry></row><row><entry /></row><row><entry>Query:</entry><entry>279</entry><entry>MADMTAIEWNEAFAVIDGLFETHYPDLLDRYNIFGGALAYGHPYGASAAIIILHLMRALE</entry><entry>338</entry></row><row><entry /><entry /><entry>+ ++  IE NEAF+      +        + NI+GGALA GHPYGAS A ++  L    +</entry></row><row><entry>Sbjct:</entry><entry>297</entry><entry>IENIEVIEINEAFSAQVVACQQALNISNTQLNIWGGALASGHPYGASGAQLVTRLFYMFD</entry><entry>356</entry></row><row><entry /></row><row><entry>Query:</entry><entry>339</entry><entry>IKNGRYGIAAIAAAGGQGFAVL</entry><entry>360</entry></row><row><entry /><entry /><entry> +     IA++   GG G A L</entry></row><row><entry>Sbjct:</entry><entry>357</entry><entry>KET---MIASMGIGGGLGNAAL</entry><entry>375</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00197" num="00197"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 182/362 (50%), Positives = 243/362 (66%), Gaps = 2/362 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>DVYIGFGLRTPIGIKGKQFKHYRPELLGAHLLNQIKKIESESNIDSIICGNTVGTGGNIG</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>DVYI  GLRTPIG+ GKQF   +PE+LGA L+N ++  +    ID +ICGNTVGTGGNIG</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>DVYIAAGLRTPIGLVGKQFAKEQPEILGAKLINALQN-KYPVPIDQVICGNTVGTGGNIG</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>RLMTLFSDYESYIPVQTIDMQCASSSSALFFGYLKISTGINEKVLVGGIESSSLQPMRRY</entry><entry>124</entry></row><row><entry /><entry /><entry>RLMTL+S     +   T+DMQCAS+ +AL  GY KI  G+   +LVGGIESSSLQP   Y</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>RLMTLYSHLGESVSALTVDMQCASAGAALSVGYAKIKAGMASNLLVGGIESSSLQPESVY</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>AKEDNRNGEYTVAQFSPDSYAETVMLEGAQRVCQKYGFRREMLDKLAFLSHKRALTAKQG</entry><entry>184</entry></row><row><entry /><entry /><entry>A  D R G Y VAQFSPDS +   M+EGA+RV +++GF +E L+     SH++A   ++</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>ASADWRQGAYKVAQFSPDSISPFAMIEGAERVAREHGFTKEYLNHWTLRSHQKASYCQEQ</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>GYLEEVILPMEGMRDQGVR-KLKETFFQKLPRLMENSPLLTIGNVCLMHDAAAFLTLQSQ</entry><entry>243</entry></row><row><entry /><entry /><entry>  L ++IL + G  DQG+R +L      K+P ++    +++  N CL HDAAAFL L SQ</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>ALLADLILDLSGASDQGIRPRLSSKVLSKVPPILGEGHVISAANACLTHDAAAFLQLSSQ</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>244</entry><entry>KTEFRIVHIVEVAGDPKLSPELVHTATEKLLTETHTKISDYDAIEWNEPFAAIDALFNHY</entry><entry>303</entry></row><row><entry /><entry /><entry> + F+++ +VEVAGDP+ SP +V  A++ LL +    ++D  AIEWNE FA ID LF  +</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>PSAFKLIDVVEVAGDPQRSPLMVIKASQVLLEKHGLGMADMTAIEWNEAFAVIDGLFETH</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>304</entry><entry>YPEEREKFNIFGGTLAYGHPYACSGIINILHLMQALKYKNKPMGLTAIAGAGGVGMAISIEY</entry><entry>365</entry></row><row><entry /><entry /><entry>YP+  +++NIFGG LAYGHPY  S  I ILHLM+AL+ KN   G+ AIA AGG G A+ ++Y</entry></row><row><entry>Sbjct:</entry><entry>302</entry><entry>YPDLLDRYNIFGGALAYGHPYGASAAIIILHLMRALEIKNGRYGIAAIAAAGGQGFAVLLKY</entry><entry>363</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 59

A DNA sequence (GBSx0058) was identified in <i>S. agalactiae </i>&lt;SEQ ID 183&gt; which encodes the amino acid sequence &lt;SEQ ID 184&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00198" num="00198"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.82</entry><entry>Transmembrane</entry><entry>149-165 (148-165)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2529(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00199" num="00199"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB12876 GB: Z99109 similar to long-chain fatty-acid-CoA ligase</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 90/382 (23%), Positives = 158/382 (40%), Gaps = 24/382 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>47</entry><entry>ISTHSLLNQLVRFVSKLCQKALPIICKPNLTHNEISRLEKEV--QYAPQLADFGVLSSGT</entry><entry>104</entry><entry /></row><row><entry /><entry /><entry>IS   L+  L  F +KL     P++   N    +IS    +      P+   +   +SG+</entry></row><row><entry>Sbjct:</entry><entry>95</entry><entry>ISNADLVVTLAFFKNKLTDSQTPVVLLDNCMA-DISEAAADPLPTIDPEHPFYMGFTSGS</entry><entry>153</entry></row><row><entry /></row><row><entry>Query:</entry><entry>105</entry><entry>TADAKLLWRSFTSWSDFFSIQNAYFSVTSNSKLFIQGDFSFTGNLNLALSLLLLGGTLVV</entry><entry>164</entry></row><row><entry /><entry /><entry>T   K   RS  SW + F+     FS++S+ K+ I G    +  L  A+S L LGGT+ +</entry></row><row><entry>Sbjct:</entry><entry>154</entry><entry>TGKPKAFTRSHRSWMESFTCTETDFSISSDDKVLIPGALMSSHFLYGAVSTLFLGGTVCL</entry><entry>213</entry></row><row><entry /></row><row><entry>Query:</entry><entry>165</entry><entry>TQKNSVKYWQTLWEKTGVTHLYLLPSYLKLVEQYSKETALDNKTIITSSQYVSDSLLEGL</entry><entry>224</entry></row><row><entry /><entry /><entry> +K S    +    +  ++ LY +P+    + +         K I + + + ++S  + L</entry></row><row><entry>Sbjct:</entry><entry>214</entry><entry>LKKFSPAKAKEWLCRESISVLYTVPTMTDALARIEGFPDSPVKIISSGADWPAES-KKKL</entry><entry>272</entry></row><row><entry /></row><row><entry>Query:</entry><entry>225</entry><entry>YRKHPKVSVKIFYGASELNYVSWYDGRDIRDKPQYVGEIVPNVAVRIKE-----------</entry><entry>273</entry></row><row><entry /><entry /><entry>    P + +  FYG SEL++V++    D + KP   G    NV + I+</entry></row><row><entry>Sbjct:</entry><entry>273</entry><entry>AAAWPHLKLYDFYGTSELSFVTFSSPEDSKRKPHSAGRPFHNVRIEIRNAGGERCQPGEI</entry><entry>332</entry></row><row><entry /></row><row><entry>Query:</entry><entry>274</entry><entry>GRIFVKTPYSICG-----LSSEYCAGDYGELID--GKLYLFGRGGDWCNQSGIKLYLPRL</entry><entry>326</entry></row><row><entry /><entry /><entry>G+IFVK+P    G        E+   D    +D  G LY+ GR        G+ ++   +</entry></row><row><entry>Sbjct:</entry><entry>333</entry><entry>GKIFVKSPMRFSGYVNGSTPDEWMTVDDMGYVDEEGFLYISGRENGMIVYGGLNIFPEEI</entry><entry>392</entry></row><row><entry /></row><row><entry>Query:</entry><entry>327</entry><entry>IEKIKTCPYIKDAVAFTKESQSHGQESHCCIVLIENQMQQECLKWLSEHFEKKYGFKHYH</entry><entry>386</entry></row><row><entry /><entry /><entry>   +  CP ++ A       +  G+ +    V++ N   +    W  +        K +</entry></row><row><entry>Sbjct:</entry><entry>393</entry><entry>ERVLLACPEVESAAVVGIPDEYWGEIA--VAVILGNANARTLKAWCKQKLASYKIPKKWV</entry><entry>450</entry></row><row><entry /></row><row><entry>Query:</entry><entry>387</entry><entry>IVSKIPLMPSGKIDYQQLKRQL</entry><entry>408</entry></row><row><entry /><entry /><entry>    +P   SGKI   ++K+ L</entry></row><row><entry>Sbjct:</entry><entry>451</entry><entry>FADSLPETSSGKIARSRVKKWL</entry><entry>472</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 185&gt; which encodes the amino acid sequence &lt;SEQ ID 186&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00200" num="00200"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 52</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2487(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00201" num="00201"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 154/413 (37%), Positives = 235/413 (56%), Gaps = 9/413 (2%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLESLKTIVKTNSDKKLFDGD-LQVSYGEFYNLVR-QDMASQDNRKHVISTHSLLNQLVR</entry><entry>58</entry><entry /></row><row><entry /><entry /><entry>ML  L+   K   +KK    D + ++Y E +  V  +D   +D+  ++IS    LNQL+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLTKLEYWAKQCPNKKAIVADQISLTYQELWQAVLIKDQTIKDSVPYIISHSRYLNQLLS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>59</entry><entry>FVSKLCQKALPIICKPNLT---HNEISRLEKEVQYAPQLADFGVLSSGTTADAKLLWRSF</entry><entry>115</entry></row><row><entry /><entry /><entry>F+  L + + PII  PN++     +I  ++ E+    + ADF VLSSGTT  AKL WR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FLRGLKEGSCPIILHPNISGTFQQQIKHVDGELL---KKADFAVLSSGTTGKAKLFWRRL</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>116</entry><entry>TSWSDFFSIQNAYFSVTSNSKLFIQGDFSFTGNLNLALSLLLLGGTLVVTQKNSVKYWQT</entry><entry>175</entry></row><row><entry /><entry /><entry>++W+  F  QN  F +T NS LF+ G FSFTGNLNLAL+ L  GG LV++QK S+K W +</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>STWTRLFDYQNKVFGMTGNSCLFLHGSFSFTGNLNLALAQLWAGGCLVLSQKLSLKTWLS</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>LWEKTGVTHLYLLPSYLKLVEQYSKETALDNKTIITSSQYVSDSLLEGLYRKHPKVSVKI</entry><entry>235</entry></row><row><entry /><entry /><entry>LW+   V+HLYLLP+YL  +  Y  +  +    ++TSSQ +S  LL   Y+K P++ + I</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>LWQAKKVSHLYLLPTYLNRLLPYLTKNNMTATHLLTSSQMISQELLRHYYKKFPQLEIVI</entry><entry>237</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>FYGASELNYVSWYDGRDIRDKPQYVGEIVPNVAVRIKEGRIFVKTPYSICGLSSEYCAGD</entry><entry>295</entry></row><row><entry /><entry /><entry>FYGASEL++++W +GR        VG+  P+V++  K+  IFV+TPYS+ G+S  Y   D</entry></row><row><entry>Sbjct:</entry><entry>238</entry><entry>FYGASELSFITWCNGRAAVKINGLVGQPFPDVSISFKDKEIFVETPYSVEGMSQPYSVSD</entry><entry>297</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>YGELIDGKLYLFGRGGDWCNQSGIKLYLPRLIEKIKTCPYIKDAVAFTKESQSHGQESHC</entry><entry>355</entry></row><row><entry /><entry /><entry> G++    L L GR  DW NQ G+K +LP L+E     P +K+A A  K  +   +</entry></row><row><entry>Sbjct:</entry><entry>298</entry><entry>LGKMSPAGLILEGRQDDWVNQRGVKCHLPSLVELAHQAPNVKEAHAL-KIGKGENETLIL</entry><entry>356</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>CIVLIENQMQQECLKWLSEHFEKKYGFKHYHIVSKIPLMPSGKIDYQQLKRQL</entry><entry>408</entry></row><row><entry /><entry /><entry> +VL +         +L+ +       K+Y ++  +PL  +GKI+ + L  ++</entry></row><row><entry>Sbjct:</entry><entry>357</entry><entry>VLVLTKKDCLAPIKDFLALYLNSGQLPKYYLVIDCLPLKDNGKINREVLLNKI</entry><entry>409</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 60

A DNA sequence (GBSx0059) was identified in <i>S. agalactiae </i>&lt;SEQ ID 187&gt; which encodes the amino acid sequence &lt;SEQ ID 188&gt;. This protein is predicted to be endonuclease III (pdg). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00202" num="00202"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.00</entry><entry>Transmembrane</entry><entry>25-41 (25-41)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1001(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00203" num="00203"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05417 GB: AP001512 endonuclease III (DNA repair) [<i>Bacillus</i></entry><entry /></row><row><entry><i>halodurans</i>]</entry></row><row><entry>Identities = 95/202 (47%), Positives = 134/202 (66%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLSKAKSRYIIREIIKLFPDAKPSLDFTNVFELLVAVMLSAQTTDAAVNKVTPALFERFP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>ML+K +++  +  I  ++PDA+  L  +N FELL+AV+LSAQ TDA VNKVTP LF ++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLTKKQTQEALAVIADMYPDAECELTHSNPFELLIAVVLSAQCTDALVNKVTPRLFAKYK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NPLVLAQADPKEIEPYISKIGLYRNKARFLNQCAKQLIEHFDGKVPRTRQELESLAGVGR</entry><entry>120</entry></row><row><entry /><entry /><entry> P        +E+E  I  IGLYRNKA+ + +  + L+E + G+VP+ R EL  LAGVGR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TPEDYIAVPLEELEQDIRSIGLYRNKAKNIKKLCQSLLEQYGGEVPQDRDELVKLAGVGR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>KTANVVMSVGFGIPAFAVDTHVTRICKHHQICKQSASPLEIEKRVMEVLPPEEWLAAHQS</entry><entry>180</entry></row><row><entry /><entry /><entry>KTANVV SV FG+PA AVDTHV R+ K   IC+   +  ++E+ +M+ +P +EW  +H</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>KTANVVASVAFGVPAIAVDTHVERVSKRLGICRWKDNVTQVEQTLMKKIPMDEWSISHHR</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>MIYFGRAICHPKNPKCDQYPQL</entry><entry>202</entry></row><row><entry /><entry /><entry>+I+FGR  C  +NP+CD  P L</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LIFFGRYHCKAQNPQCDICPLL</entry><entry>202</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 189&gt; which encodes the amino acid sequence &lt;SEQ ID 190&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00204" num="00204"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00205" num="00205"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 91/199 (45%), Positives = 133/199 (66%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>LSKAKSRYIIREIIKLFPDAKPSLDFTNVFELLVAVMLSAQTTDAAVNKVTPALFERFPN</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+ KA+   ++  I ++FP+AK  LD+   F+LL+AV+LSAQTTD AVNKVTP L++ +P</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>IGKARLAKVLTIIGQMFPEAKGELDWETPFQLLIAVILSAQTTDKAVNKVTPGLWQSYPE</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>PLVLAQADPKEIEPYISKIGLYRNKARFLNQCAKQLIEHFDGKVPRTRQELESLAGVGRK</entry><entry>121</entry></row><row><entry /><entry /><entry>   LA A+  ++E  +  IGLY+NKA+ + + A+ + + F G+VP+T +ELESL GVGRK</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>IEDLAFAELSDVENALRTIGLYKNKAKNIIKTAQAIRDDFKGQVPKTHKELESLPGVGRK</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>TANVVMSVGFGIPAFAVDTHVTRICKHHQICKQSASPLEIEKRVMEVLPPEEWLAAHQSM</entry><entry>181</entry></row><row><entry /><entry /><entry>TANVV++  +G+PA AVDTHV R+ K   I    A   +IE  +M  +P ++W+  H  +</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>TANVVLAEVYGVPAIAVDTHVARVSKRLNISSPDADVKQIEADLMAKIPKKDWIITHHRL</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>IYFGRAICHPKNPKCDQYP</entry><entry>200</entry></row><row><entry /><entry /><entry>I+FGR  C  K PKC+  P</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>IFFGRYHCLAKKPKCEICP</entry><entry>201</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 61

A DNA sequence (GBSx0060) was identified in <i>S. agalactiae </i>&lt;SEQ ID 191&gt; which encodes the amino acid sequence &lt;SEQ ID 192&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00206" num="00206"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2264 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00207" num="00207"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAA96473 GB:AB036428 hypothetical 8.3 kDa protein [<i>Streptococcus mutans</i>]</entry><entry /></row><row><entry>Identities = 53/67 (79%), Positives = 62/67 (92%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKVLFDVQNLLKKFGIYVYIGKRLYDIEVMKIELQRLYDNGLISRDDYLKAELILRREHR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MK L+DVQ LLK+FGI+VY+GKRLYDIE+MKIEL+RLYDNGLIS+ DYL AELILRREHR</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKTLYDVQRLLKQFGIFVYLGKRLYDIEMMKIELERLYDNGLISKSDYLHAELILRREHR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LELEKEN</entry><entry>67</entry></row><row><entry /><entry /><entry>+E E+EN</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>IEKEREN</entry><entry>67</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 193&gt; which encodes the amino acid sequence &lt;SEQ ID 194&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00208" num="00208"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1962 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00209" num="00209"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 53/66 (80%), Positives = 60/66 (90%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKVLFDVQNLLKKFGIYVYIGKRLYDIEVMKIELQRLYDNGLISRDDYLKAELILRREHR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MK L+DVQ LLK FGI+VY+GKRLYDIE+MKIELQRLYD+GL+ + DYL AELILRREHR</entry></row><row><entry>Sbjct:</entry><entry>7</entry><entry>MKTLYDVQQLLKNFGIFVYLGKRLYDIEMMKIELQRLYDSGLLDKRDYLNAELILRREHR</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LELEKE</entry><entry>66</entry></row><row><entry /><entry /><entry>LELEKE</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>LELEKE</entry><entry>72</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 62

A DNA sequence (GBSx0061) was identified in <i>S. agalactiae </i>&lt;SEQ ID 195&gt; which encodes the amino acid sequence &lt;SEQ ID 196&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00210" num="00210"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.06</entry><entry>Transmembrane</entry><entry>133-149 (133-150)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1022(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00211" num="00211"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB05144 GB: AP001512 glucose kinase [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 145/315 (46%), Positives = 209/315 (66%), Gaps = 2/315 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>LGIDLGGTTIKFGILTLEGEVQEKWAIETNTLENGRHIVSDIVESLKHRLSLYGLTKDDF</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>+G+D+GGTTIK   LT  GE+ +KW I TN  + G  I ++I ++L  RLS +  +K D</entry></row><row><entry>Sbjct:</entry><entry>7</entry><entry>VGVDVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHKSKSDL</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>LGIGMGSPGAVDRTSKTVTGAFNLNWADTQEVGSVIEKEVGIPFFIDNDANVAALGERWV</entry><entry>125</entry></row><row><entry /><entry /><entry>+GIG+G+PG ++  +  +  A N+ W D   +   +E+E  +P  +DNDAN+AALGE W</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>IGIGLGAPGFIEMDTGFIYHAVNIGWRDFP-LKDKLEEETKLPVIVDNDANIAALGEMWK</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>GAGANNPDVVFVTLGTGVGGGVIADGNLIHGVAGAGGEIGHMIVDPENGFTCTCGNKGCL</entry><entry>185</entry></row><row><entry /><entry /><entry>GAG    +++ +TLGTGVGGG++A+GN++HGV G  GEIGH+ V PE G  C CG  GCL</entry></row><row><entry>Sbjct:</entry><entry>126</entry><entry>GAGDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCGKTGCL</entry><entry>185</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>ETVASATGVVRVARQLAEQYEGSSAIKAAIDNGDTVTSKDIFIAAEDGDKFANSVVERVS</entry><entry>245</entry></row><row><entry /><entry /><entry>ETVASATG+ R+A +   +++  S +    D    +T+KD+F AA+  D FA SVV+ ++</entry></row><row><entry>Sbjct:</entry><entry>186</entry><entry>ETVASATGIARIATEGVTEHK-ESQLALDYDKHGVLTAKDVFSAADASDAFALSVVDHIA</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>RYLGLAAANISNILNPDSVVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIKIAELG</entry><entry>305</entry></row><row><entry /><entry /><entry> YLG A AN++N LNP+ +VIGGGVS AG+ L   ++++F  +A P+V    + +IA LG</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>YYLGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRIATLG</entry><entry>304</entry></row><row><entry /></row><row><entry>Query:</entry><entry>306</entry><entry>NDAGIIGAASLANQQ</entry><entry>320</entry></row><row><entry /><entry /><entry>NDAG+IG   L  QQ</entry></row><row><entry>Sbjct:</entry><entry>305</entry><entry>NDAGVIGGGWLVKQQ</entry><entry>319</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 197&gt; which encodes the amino acid sequence &lt;SEQ ID 198&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00212" num="00212"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1060(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00213" num="00213"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 270/319 (84%), Positives = 292/319 (90%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKKLLGIDLGGTTIKFGILTLEGEVQEKWAIETNTLENGRHIVSDIVESLKHRLSLYGL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MS+KLLGIDLGGTTIKFGILT  GEVQEKWAIETN LE G+HIV DI+ S+KHRL LYGL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSQKLLGIDLGGTTIKFGILTAAGEVQEKWAIETNILEGGKHIVPDIIASIKHRLDLYGL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TKDDFLGIGMGSPGAVDRTSKTVTGAFNLNWADTQEVGSVIEKEVGIPFFIDNDANVAAL</entry><entry>120</entry></row><row><entry /><entry /><entry>+  DF+GIGMGSPGAVDR + TVTGAFNLNW +TQEVGSV+EKE+GIPF IDNDANVAAL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>SSADFVGIGMGSPGAVDRDTNTVTGAFNLNWKETQEVGSVVEKELGIPFAIDNDANVAAL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GERWVGAGANNPDVVFVTLGTGVGGGVIADGNLIHGVAGAGGEIGHMIVDPENGFTCTCG</entry><entry>180</entry></row><row><entry /><entry /><entry>GERWVGAG NNPDVVF+TLGTGVGGG+IADGNLIHGVAGAGGEIGHMIV+PENGF CTCG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GERWVGAGENNPDVVFMTLGTGVGGGIIADGNLIHGVAGAGGEIGHMIVEPENGFACTCG</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>NKGCLETVASATGVVRVARQLAEQYEGSSAIKAAIDNGDTVTSKDIFIAAEDGDKFANSV</entry><entry>240</entry></row><row><entry /><entry /><entry>+ GCLETVASATGVV+VAR LAE YEG SAIKAAIDNG+ VTSKDIF+AAE GD FA+SV</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SHGCLETVASATGVVKVARLLAEAYEGDSAIKAAIDNGEGVTSKDIFMAAEAGDSFADSV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VERVSRYLGLAAANISNILNPDSVVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIK</entry><entry>300</entry></row><row><entry /><entry /><entry>VE+V  YLGLA+ANISNILNPDSVVIGGGVSAAGEFLRSR+EKYFVTF FPQV+ STKIK</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>VEKVGYYLGLASANISNILNPDSVVIGGGVSAAGEFLRSRIEKYFVTFTFPQVRYSTKIK</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>IAELGNDAGIIGAASLANQ</entry><entry>319</entry></row><row><entry /><entry /><entry>IAELGNDAGIIGAASLA Q</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>IAELGNDAGIIGAASLARQ</entry><entry>319</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 63

A DNA sequence (GBSx0062) was identified in <i>S. agalactiae </i>&lt;SEQ ID 199&gt; which encodes the amino acid sequence &lt;SEQ ID 200&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00214" num="00214"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00215" num="00215"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14385 GB: Z99116 similar to hypothetical proteins [<i>Bacillus</i></entry><entry /></row><row><entry><i>subtilis</i>]</entry></row><row><entry>Identities = 51/124 (41%), Positives = 71/124 (57%), Gaps = 1/124 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKHIL</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>MS +++++I  AF+ +   +Y   +R  K L  E F+    + QLID+RE   F   HIL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSNMIVLIIFPAFIIYMIASYVYQQRIMKTLTEEEFRAGYRKAQLIDVREPNEFEGGHIL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>GARNIPASQFKVALSALRKDKPVLLYDASRGQSIPRIVLLLRKEGFNQLYVLKDGFNYWT</entry><entry>122</entry></row><row><entry /><entry /><entry>GARNIP SQ K   + +R DKPV LY  +  +S  R    LRK G  ++Y LK GF  W</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GARNIPLSQLKQRKNEIRTDKPVYLYCQNSVRS-GRAAQTLRKNGCTEIYNLKGGFKKWG</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>GRVK</entry><entry>126</entry></row><row><entry /><entry /><entry>G++K</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>GKIK</entry><entry>123</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 201&gt; which encodes the amino acid sequence &lt;SEQ ID 202&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00216" num="00216"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.41</entry><entry>Transmembrane</entry><entry>4-20 (1-22)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2763 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00217" num="00217"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB06532 GB:AP001516 unknown conserved protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 46/120 (38%), Positives = 64/120 (53%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>LWLLLVGIVGYYTWNYFSFRKMAKQVDNETFKDVMRQGQLIDLREPAAFRTKHILGARNF</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>+WL+L+ ++ Y  +      K  K +  E F    R+ QLID+REP  + + HILGARN</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>VWLVLLALLVYVLFKRLYTPKYLKTLTQEEFIQGYRKAQLIDVREPREYDSGHILGARNI</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>PAQQFDAAIKGLRKDKPVLIYENMRPQYRVPAVKKLKKAGFEDVYVLKDGIDYWDGKVKQ</entry><entry>127</entry></row><row><entry /><entry /><entry>P  Q    +K +R D+PV +Y     + R  A    KK G EDV  LK G   W GK+K+</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>PLSQLKQRLKEVRTDQPVYLYCQSGARSRQAAAILKKKHGVEDVNHLKGGFRKWTGKIKK</entry><entry>124</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00218" num="00218"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 63/126 (50%), Positives = 85/126 (67%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MDMSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKH</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M    +++ ++L+  V + +WNY+  R+ AK +DNE+F+  M +GQLID+RE  AF  KH</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSPITLILWLLLVGIVGYYTWNYFSFRKMAKQVDNETFKDVMRQGQLIDLREPAAFRTKH</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>ILGARNIPASQFKVALSALRKDKPVLLYDASRGQSIPRIVLLLRKEGFNQLYVLKDGFNY</entry><entry>120</entry></row><row><entry /><entry /><entry>ILGARN PA QF  A+  LRKDKPVL+Y+  R Q     V  L+K GF  +YVLKDG +Y</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ILGARNFPAQQFDAAIKGLRKDKPVLIYENMRPQYRVPAVKKLKKAGFEDVYVLKDGIDY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>WTGRVK</entry><entry>126</entry></row><row><entry /><entry /><entry>W G+VK</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>WDGKVK</entry><entry>126</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8483&gt; and protein &lt;SEQ ID 8484&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00219" num="00219"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 1</entry><entry /></row><row><entry>McG: Discrim Score: 17.55</entry></row><row><entry>GvH: Signal Score (−7.5): 3.36</entry></row><row><entry>Possible site: 17</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="49pt" align="left" /><colspec colname="4" colwidth="189pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 0</entry><entry>value: 8.86</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="203pt" align="left" /><colspec colname="4" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 8.86</entry><entry>99</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −2.27</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00011" num="00011"><img id="EMI-C00011" he="100.25mm" wi="120.06mm" file="US07939087-20110510-C00011.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00011" attachment-type="cdx" file="US07939087-20110510-C00011.CDX" /><attachment idref="CHEM-US-00011" attachment-type="mol" file="US07939087-20110510-C00011.MOL" /></attachments></chemistry>

SEQ ID 8484 (GBS13) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 3</figref> (lane 4; MW 16 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 9</figref> (lane 2; MW 40.5 kDa).

The GST-fusion protein was purified as shown in <figref idrefs="DRAWINGS">FIG. 190</figref>, lane 5.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 64

A DNA sequence (GBSx0063) was identified in <i>S. agalactiae </i>&lt;SEQ ID 203&gt; which encodes the amino acid sequence &lt;SEQ ID 204&gt;. This protein is predicted to be regulatory protein TypA (typA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00220" num="00220"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="308pt" align="left" /><colspec colname="2" colwidth="133pt" align="left" /><tbody valign="top"><row><entry>Possible Site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>    bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) &lt;succ&gt;</entry></row><row><entry>      bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>        bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00221" num="00221"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB13350 GB:Z99111 similar to GTP-binding elongation factor</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 455/609 (74%), Positives = 534/609 (86%), Gaps = 2/609 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:   4</entry><entry>LRTDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELEERAMDSNDIEKERGITILAKN</entry><entry>63</entry><entry /></row><row><entry /><entry>LR D+RN+AIIAHVDHGKTTLVD+LL Q+ T    +++ ERAMDSND+E+ERGITILAKN</entry></row><row><entry>Sbjct:   3</entry><entry>LRNDLRNIAIIAHVDHGKTTLVDQLLHQAGTFRANEQVAERAMDSNDLERERGITILAKN</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:  64</entry><entry>TAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKALEQN</entry><entry>123</entry></row><row><entry /><entry>TA+ Y D RINI+DTPGHADFGGEVERIMKMVDGVVLVVDAYEG MPQTRFVLKKALEQN</entry></row><row><entry>Sbjct:  63</entry><entry>TAINYKDTRINILDTPGHADFGGEVERIMKMVDGVVLVVDAYEGCMPQTRFVLKKALEQN</entry><entry>122</entry></row><row><entry /></row><row><entry>Query: 124</entry><entry>LIPIVVVNKIDKPSARPSEVVDEVLELFIELGADDDQLDFPVVYASAINGTSSMSDDPSD</entry><entry>183</entry></row><row><entry /><entry>L P+VVVNKID+  ARP EV+DEVL+LFIEL A+++QL+FPVVYASAINGT+S+   DP</entry></row><row><entry>Sbjct: 123</entry><entry>LNPVVVVNKIDRDFARPEEVIDEVLDLFIELDANEEQLEFPVVYASAINGTASL--DPKQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query: 184</entry><entry>QEKTMAPIFDTIIDHIPAPVDNSEEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGDQVT</entry><entry>243</entry></row><row><entry /><entry>Q++ M  +++TII H+PAPVDN+EEPLQFQV+LLDYND+VGRIGIGRVFRGT+KVG  QV+</entry></row><row><entry>Sbjct: 181</entry><entry>QDENMEALYETIIKHVPAPVDNAEEPLQFQVALLDYNDYVGRIGIGRVFRGTMKVGQQVS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query: 244</entry><entry>LSKLDGTTKNFRVTKLFGFFGLERKEIQEAKAGDLIAVSGMEDIFVGETVTPTDAIEPLP</entry><entry>303</entry></row><row><entry /><entry>L KLDGT K+FRVTK+FGF GL+R EI+EAKAGDL+AVSGMEDI VGETV P D  +PLP</entry></row><row><entry>Sbjct: 241</entry><entry>LMKLDGTAKSFRVTKIFGFQGLKRVEIEEAKAGDLVAVSGMEDINVGETVCPVDHQDPLP</entry><entry>300</entry></row><row><entry /></row><row><entry>Query: 304</entry><entry>VLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDKWTV</entry><entry>363</entry></row><row><entry /><entry>VLRIDEPTLQMTF+VNNSPFAGREGK++T+RK+EERL ++LQTDVSLRV+PT SPD W V</entry></row><row><entry>Sbjct: 301</entry><entry>VLRIDEPTLQMTFVVNNSPFAGREGKYVTARKIEERLQSQLQTDVSLRVEPTASPDAWVV</entry><entry>360</entry></row><row><entry /></row><row><entry>Query: 364</entry><entry>SGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCEPFERVQIDTPEEYQGAIIQS</entry><entry>423</entry></row><row><entry /><entry>SGRGELHLSILIE MRREGYELQVS+PEVIIKEIDGV+CEP ERVQID PEE+ G++++S</entry></row><row><entry>Sbjct: 361</entry><entry>SGRGELHLSILIENMRREGYELQVSKPEVIIKEIDGVRCEPVERVQIDVPEEHTGSVMES</entry><entry>420</entry></row><row><entry /></row><row><entry>Query: 424</entry><entry>LSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPVVQG</entry><entry>483</entry></row><row><entry /><entry>+  RKG+M+DM   GNGQ RLIF +P+RGLIGYSTEFLS+TRG+GI+NHTFD Y P+  G</entry></row><row><entry>Sbjct: 421</entry><entry>MGARKGEMVDMINNGNGQVRLIFTVPSRGLIGYSTEFLSLTRGFGILNHTFDSYQPMQAG</entry><entry>480</entry></row><row><entry /></row><row><entry>Query: 484</entry><entry>EIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGIEVYEGMIVGENSRDNDLGVNIT</entry><entry>543</entry></row><row><entry /><entry>++GGR +G LVS+ENGKAT+Y I  IE+RG IFV PG EVYEGMIVGE++RDNDL VN++</entry></row><row><entry>Sbjct: 481</entry><entry>QVGGRRQGVLVSMENGKATSYGIQGIEDRGVIFVEPGTEVYEGMIVGEHNRDNDLVVNVS</entry><entry>540</entry></row><row><entry /></row><row><entry>Query: 544</entry><entry>TAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLADDEYMEVTPESIRLRKQILNKAARD</entry><entry>603</entry></row><row><entry /><entry>  KQ TNVRSATKDQT  IK  RI++LEESLE+L +DEY EVTPESIRLRK+ILNK  R+</entry></row><row><entry>Sbjct: 541</entry><entry>KMKQQTNVRSATKDQTTTIKKARIMSLEESLEYLNEDEYCEVTPESIRLRKKILNKNERE</entry><entry>600</entry></row><row><entry /></row><row><entry>Query: 604</entry><entry>KANKKKKSA</entry><entry>612</entry></row><row><entry /><entry>KA KKKK+A</entry></row><row><entry>Sbjct: 601</entry><entry>KAAKKKKTA</entry><entry>609</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 205&gt; which encodes the amino acid sequence &lt;SEQ ID 206&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00222" num="00222"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="308pt" align="left" /><colspec colname="2" colwidth="133pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-termina1 signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>    bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) &lt;succ&gt;</entry></row><row><entry>      bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>    bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00223" num="00223"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 594/613 (96%), Positives = 607/613 (98%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTNLRTDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELEERAMDSNDIEKERGITIL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTNLR DIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKEL+ERAMDSND+EKERGITIL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTNLRNDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELQERAMDSNDLEKERGITIL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL</entry><entry>120</entry></row><row><entry /><entry /><entry>AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>EQNLIPIVVVNKIDKPSARPSEVVDEVLELFIELGADDDQLDFPVVYASAINGTSSMSDD</entry><entry>180</entry></row><row><entry /><entry /><entry>EQNLIPIVVVNKIDKPSARP+EVVDEVLELFIELGADD+QL+FPVVYASAINGTSS+SDD</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>EQNLIPIVVVNKIDKPSARPAEVVDEVLELFIELGADDEQLEFPVVYASAINGTSSLSDD</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>PSDQEKTMAPIFDTIIDHIPAPVDNSEEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD</entry><entry>240</entry></row><row><entry /><entry /><entry>P+DQE TMAPIFDTIIDHIPAPVDNS+EPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>PADQEHTMAPIFDTIIDHIPAPVDNSDEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>QVTLSKLDGTTKNFRVTKLFGFFGLERKEIQEAKAGDLIAVSGMEDIFVGETVTPTDAIE</entry><entry>300</entry></row><row><entry /><entry /><entry>QVTLSKLDGTTKNFRVTKLFGFFGLER+EIQEAKAGDLIAVSGMEDIFVGET+TPTD +E</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>QVTLSKLDGTTKNFRVTKLFGFFGLERREIQEAKAGDLIAVSGMEDIFVGETITPTDCVE</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>PLPVLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK</entry><entry>360</entry></row><row><entry /><entry /><entry> LP+LRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>ALPILRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCEPFERVQIDTPEEYQGAI</entry><entry>420</entry></row><row><entry /><entry /><entry>WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGV+CEPFERVQIDTPEEYQGAI</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVKCEPFERVQIDTPEEYQGAI</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV</entry><entry>480</entry></row><row><entry /><entry /><entry>IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGIEVYEGMIVGENSRDNDLGV</entry><entry>540</entry></row><row><entry /><entry /><entry>VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPG EVYEGMIVGENSRDNDLGV</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGTEVYEGMIVGENSRDNDLGV</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLADDEYMEVTPESIRLRKQILNKA</entry><entry>600</entry></row><row><entry /><entry /><entry>NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFL DDEYMEVTPESIRLRKQILNKA</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLNDDEYMEVTPESIRLRKQILNKA</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>ARDKANKKKKSAE</entry><entry>613</entry></row><row><entry /><entry /><entry>ARDKANKKKKSAE</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>ARDKANKKKKSAE</entry><entry>613</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 65

A DNA sequence (GBSx0065) was identified in <i>S. agalactiae </i>&lt;SEQ ID 207&gt; which encodes the amino acid sequence &lt;SEQ ID 208&gt;. This protein is predicted to be D-glutamic acid adding enzyme MurD (murD). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00224" num="00224"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>RGD motif 441-443</entry><entry /></row><row><entry>Possible site: 29</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9615&gt; which encodes amino acid sequence &lt;SEQ ID 9616&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00225" num="00225"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95449 GB: AF068902 D-glutamic acid enzyme MurD [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 341/449 (75%), Positives = 394/449 (86%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MKTITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVV</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>MK I  F+NKKVLVLGLA+SGE+AARLL KLGAIVTVNDGKPF++NP AQ LLEEGIKV+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKVIDQFKNKKVLVLGLAKSGESAARLLDKLGAIVTVNDGKPFEDNPAAQCLLEEGIKVI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>CGSHPLELLDEDFCYMIKNPGIPYNNPMVKKALEKQIPVLTEVELAYLVSESQLIGITGS</entry><entry>124</entry></row><row><entry /><entry /><entry> G HPLELLDE+F  M+KNPGIPY+NPM++KAL K IPVLTEVELAYL+SE+ +IGITGS</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TGGHPLELLDEEFALMVKNPGIPYSNPMIEKALAKGIPVLTEVELAYLISEAPIIGITGS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>NGKTTTTTMIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVMELSSFQLMGVKEFR</entry><entry>184</entry></row><row><entry /><entry /><entry>NGKTTTTTMI EVL A GQ GLL+GNIG+PAS+V Q A DK+TLVMELSSFQLMGV+EF</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NGKTTTTTMIGEVLTAAGQHGLLSGNIGYPASQVAQIATDKNTLVMELSSFQLMGVQEFH</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>PHIAVITNLMPTHLDYHGSFEDYVAAKWNIQNQMSSSDFLVLNFNQGISKELAKTTKATI</entry><entry>244</entry></row><row><entry /><entry /><entry>P IAVITNLMPTH+DYHG FE+YVAAKWNIQN+M+++DFLVLNFNQ + K+LA  T+AT+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>PEIAVITNLMPTHIDYHGLFEEYVAAKWNIQNKMTAADFLVLNFNQDLVKDLASKTEATV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>VPFSTTEKVDGAYVQDKQLFYKGENIMSVDDIGVPGSHNVENALATIAVAKLAGISNQVI</entry><entry>304</entry></row><row><entry /><entry /><entry>VPFST EKVDGAY++D QL+++GE +M+ ++IGVPGSHNVENALATIAVAKL G+ NQ I</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>VPFSTLEKVDGAYLEDGQLYFRGEVVMAANEIGVPGSHNVENALATIAVAKLRGVDNQTI</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>RETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGN</entry><entry>364</entry></row><row><entry /><entry /><entry>+ETLS FGGVKHRLQ +  + G+ FYNDSKSTNILATQKALSGFDN+KV+LIAGGLDRGN</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>KETLSAFGGVKHRLQFVDDIKGVKFYNDSKSTNILATQKALSGFDNSKVVLIAGGLDRGN</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>EFDELIPDITGLKHMVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVIL</entry><entry>424</entry></row><row><entry /><entry /><entry>EFDEL+PDITGLK MV+LG+SA RVKRAA KAGV Y +A D+ DA  KAYE+A QGDV+L</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>EFDELVPDITGLKKMVILGQSAERVKRAADKAGVAYVEATDIADATRKAYELATQGDVVL</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>425</entry><entry>LSPANASWDMYKNFEVRGDEFIDTFESLR</entry><entry>453</entry></row><row><entry /><entry /><entry>LSPANASWDMY NFEVRGD FIDT   L+</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>LSPANASWDMYANFEVRGDLFIDTVAELK</entry><entry>449</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 209&gt; which encodes the amino acid sequence &lt;SEQ ID 210&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00226" num="00226"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>RGD motif: 436-438</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00227" num="00227"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 329/451 (72%), Positives = 397/451 (87%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MKTITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVV</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>MK I+ F+NKK+L+LGLA+SGEAAA+LL KLGA+VTVND KPFD+NP AQ+LLEEGIKV+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKVISNFQNKKILILGLAKSGEAAAKLLTKLGALVTVNDSKPFDQNPAAQALLEEGIKVI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>CGSHPLELLDEDFCYMIKNPGIPYNNPMVKKALEKQIPVLTEVELAYLVSESQLIGITGS</entry><entry>124</entry></row><row><entry /><entry /><entry>CGSHP+ELLDE+F YM+KNPGIPY+NPMVK+AL K+IP+LTEVELAY VSE+ +IGITGS</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>CGSHPVELLDENFEYMVKNPGIPYDNPMVKRALAKEIPILTEVELAYFVSEAPIIGITGS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>NGKTTTTTMIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVMELSSFQLMGVKEFR</entry><entry>184</entry></row><row><entry /><entry /><entry>NGKTTTTTMIA+VLNAGGQ  LL+GNIG+PAS+VVQ A   DTLVMELSSFQL+GV  FR</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NGKTTTTTMIADVLNAGGQSALLSGNIGYPASKVVQKAIAGDTLVMELSSFQLVGVNAFR</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>PHIAVITNLMPTHLDYHGSFEDYVAAKWNIQNQMSSSDFLVLNFNQGISKELAKTTKATI</entry><entry>244</entry></row><row><entry /><entry /><entry>PHIAVITNLMPTHLDYHGSFEDYVAAKW IQ QM+ SD+L+LN NQ IS  LAKTTKAT+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>PHIAVITNLMPTHLDYHGSFEDYVAAKWMIQAQMTESDYLILNANQEISATLAKTTKATV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>VPFSTTEKVDGAYVQDKQLFYKGENIMSVDDIGVPGSHNVENALATIAVAKLAGISNQVI</entry><entry>304</entry></row><row><entry /><entry /><entry>+PFST + VDGAY++D  L++K + I++  D+GVPGSHN+ENALATIAVAKL+GI++ +I</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>IPFSTQKVVDGAYLKDGILYFKEQAIIAATDLGVPGSHNIENALATIAVAKLSGIADDII</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>RETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGN</entry><entry>364</entry></row><row><entry /><entry /><entry> + LS+FGGVKHRLQ +G++  I+FYNDSKSTNILATQKALSGFDN+++ILIAGGLDRGN</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>AQCLSHFGGVKHRLQRVGQIKDITFYNDSKSTNILATQKALSGFDNSRLILIAGGLDRGN</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>EFDELIPDITGLKHMVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVIL</entry><entry>424</entry></row><row><entry /><entry /><entry>EFD+L+PD+ GLK M++LGESA R+KRAA KA V+Y +A +V +A   A+++AQ GD IL</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>EFDDLVPDLLGLKQMIILGESAERMKRAANKAEVSYLEARNVAEATELAFKLAQTGDTIL</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>425</entry><entry>LSPANASWDMYKNFEVRGDEFIDTFESLRGE</entry><entry>455</entry></row><row><entry /><entry /><entry>LSPANASWDMY NFEVRGDEF+ TF+ LRG+</entry></row><row><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>LSPANASWDMYPNFEVRGDEFLATFDCLRGD</entry><entry>451</entry></row></tbody></tgroup></table></tables>

SEQ ID 208 (GBS305) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 51</figref> (lane 11; MW 53.7 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 56</figref> (lane 3; MW 79 kDa).

The GBS305-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 207</figref>, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 270</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 66

A DNA sequence (GBSx0066) was identified in <i>S. agalactiae </i>&lt;SEQ ID 211&gt; which encodes the amino acid sequence &lt;SEQ ID 212&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00228" num="00228"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>RGD motif 285-287</entry><entry /></row><row><entry>Possible site: 60</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.65</entry><entry>Transmembrane</entry><entry>74-90 (73-93)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1659(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 213&gt; which encodes the amino acid sequence &lt;SEQ ID 214&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00229" num="00229"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>  81-97 (80-100)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.16</entry><entry>Transmembrane</entry><entry>272-288 (271-288)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1532(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related sequence was also identified in GAS &lt;SEQ ID 9141&gt; which encodes the amino acid sequence &lt;SEQ ID 9142&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00230" num="00230"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="28pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="63pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.33</entry><entry>Transmembrane</entry><entry>  74-90</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.16</entry><entry>Transmembrane</entry><entry>265-281</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1532(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>RGD motif: 286-288</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00231" num="00231"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Identities = 249/358 (69%), Positives = 293/358 (81%), Gaps = 1/358 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="273pt" align="left" /><colspec colname="4" colwidth="28pt" align="char" char="." /><colspec colname="5" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MGKKIVFTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEHEQINQSGLDITFHSIA</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M KKI+FTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEH +I +SGLD+TFH+IA</entry><entry /></row><row><entry>Sbjct:</entry><entry>8</entry><entry>MPKKILFTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEHTEIEKSGLDVTFHAIA</entry><entry>67</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TGKLRRYFSWQNMLDVFKVGVGVLQSIAIIAKLRPQALFSKGGFVSVPPVVAARLLKVPV</entry><entry>120</entry></row><row><entry /><entry /><entry>TGKLRRYFSWQN+ DVFKV +G+LQS+ I+AKLRPQALFSKGGFVSVPPVVAA+LL PV</entry><entry /></row><row><entry>Sbjct:</entry><entry>68</entry><entry>TGKLRRYFSWQNLADVFKVALGLLQSLFIVAKLRPQALFSKGGFVSVPPVVAAKLLGKPV</entry><entry>127</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>FVHESDLSMGLANKIAYKFATIMYTTFEQSKDLIKTKHIGAVTKVM-DCKKSFENTDLTS</entry><entry>179</entry></row><row><entry /><entry /><entry>F+HESD SMGLANKIAYKFAT MYTTFEQ L K KH+GAVTKV D + E+T L +</entry><entry /></row><row><entry>Sbjct:</entry><entry>128</entry><entry>FIHESDRSMGLANKIAYKFATTMYTTFEQEDQLSKVKHLGAVTKVFKDANQMPESTQLEA</entry><entry>187</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>IKEAFDPNLKTLLFIGGSAGAKVFNDFITQTPELEEKYNVINISGDSSLNRLKKNLYRVD</entry><entry>239</entry></row><row><entry /><entry /><entry>+KE F +LKTLLFIGGSAGA VFN FI+ PEL+++YN+INI+GD LN L +LYRVD</entry><entry /></row><row><entry>Sbjct:</entry><entry>188</entry><entry>VKEYFSRDLKTLLFIGGSAGAHVFNQFISDHPELKQRYNIINITGDPHLNELSSHLYRVD</entry><entry>247</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>YVTDLYQPLMNLADVVVTRGGSNTIFELVAMKKLHLIIPLGREASRGDQLENAAYFEEKG</entry><entry>299</entry></row><row><entry /><entry /><entry>YVTDLYQPLM +AD+VVTRGGSNT+FEL+AM KLHLI+PLG+EASRGDQLENA YFE++G</entry><entry /></row><row><entry>Sbjct:</entry><entry>248</entry><entry>YVTDLYQPLMAMADLVVTRGGSNTLFELLAMAKLHLIVPLGKEASRGDQLENATYFEKRG</entry><entry>307</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>YALQLPESELNINTLEKQINLLISNSESYEKNMSQSSEIKSQDEFYQLLIDDMAKVTK</entry><entry>357</entry></row><row><entry /><entry /><entry>YA QL E +L ++ ++ + L + YE M + EI+S D FY LL  D++ K</entry><entry /></row><row><entry>Sbjct:</entry><entry>308</entry><entry>YAKQLQEPDLTLHNFDQAMADLFEHQADYEATMLATKEIQSPDFFYDLLRADISSAIK</entry><entry>365</entry></row></tbody></tgroup></table></tables>

SEQ ID 212 (GBS306) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 51</figref> (lane 12; MW 43 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 56</figref> (lane 4; MW 68 kDa).

GBS306-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 207</figref>, lane 9.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 67

A DNA sequence (GBSx0067) was identified in <i>S. agalactiae </i>&lt;SEQ ID 215&gt; which encodes the amino acid sequence &lt;SEQ ID 216&gt;. This protein is predicted to be cell division protein DivIB. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00232" num="00232"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="84pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −14.33</entry><entry>Transmembrane</entry><entry>103-119 (96-124)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6731(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00233" num="00233"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95451 GB:AF068902 cell division protein DivIB [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 119/396 (30%), Positives = 214/396 (53%), Gaps = 38/396 (9%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="280pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KKKSDTPEKEEVV-LTEWQKRNLEFLKKRKEDEE---EQKRINEKLRLDKRS-----KLN</entry><entry>53</entry><entry /></row><row><entry /><entry /><entry>KK  D EE+  L+EWQKRN E+LKK+ E+E E+K + R+ + S K +</entry><entry /></row><row><entry>Sbjct:</entry><entry>5</entry><entry>KKNEDKEILEELKELSEWQKRNQEYLKKKAEEEAALAEEKEKERQARMGEESEKSEDKQD</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>54</entry><entry>ISSPEEPQNTTKIKKLHFPKIS------------RPKIEKKQKKEKIVNSLAKTNR----</entry><entry>97</entry></row><row><entry /><entry /><entry>  S  + +++  K+ K++  P+ ++K++++K ++  A   +</entry><entry /></row><row><entry>Sbjct:</entry><entry>65</entry><entry>QESETDQEDSESAKEESEEKVASSEADKEKEEKEEPESKEKEEQDKKLSKKATKEKPAKA</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>98</entry><entry>-------IRTAPIFVVAFLVILVSVFLLTPFSKQKTITVSGNQHTPDDILIEKTNIQKND</entry><entry>150</entry></row><row><entry /><entry /><entry> +R I + L+++VS +LL+P++ K I V G T  D + + + IQ +D</entry><entry /></row><row><entry>Sbjct:</entry><entry>125</entry><entry>KIPGIHILRAFTILFPSLLLLIVSAYLLSPYATMKDIRVEGTVQTTADDIRQASGIQDSD</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>151</entry><entry>YFFSLIFKHKAIEQRLAAEDVWVKTAQMTYQFPNKFHIQVQENKIIAYAHTKQGYQPVLE</entry><entry>210</entry></row><row><entry /><entry /><entry>Y +L+  E+++ + + WV++AQ+ YQFP KF I+V+E I+AY + + + P+L</entry><entry /></row><row><entry>Sbjct:</entry><entry>185</entry><entry>YTINLLLDKAKYEKQIKS-NYWVESAQLVYQFPTKFTIKVKEYDIVAYYISGENHYPILS</entry><entry>243</entry></row><row><entry /></row><row><entry>Query:</entry><entry>211</entry><entry>TGK-KADPVNSSELPKHFLTINLDKEDSIKLLIKDLKALDPDLISEIQVISLADSKTTPD</entry><entry>269</entry></row><row><entry /><entry /><entry>+G+ + V+ + LP+ +L++ + + IK+ + +L  + P+L + IQ + LA SK T D</entry><entry /></row><row><entry>Sbjct:</entry><entry>244</entry><entry>SGQLETSSVSLNSLPETYLSVLFNDSEQIKVFVSELAQISPELKAAIQKVELAPSKVTSD</entry><entry>303</entry></row><row><entry /></row><row><entry>Query:</entry><entry>270</entry><entry>LLLLDMHDGNSIRIPLSKFKERLPFYKQIKKNLKEPSIVDMEVGVYTTTNTIESTPVKAE</entry><entry>329</entry></row><row><entry /><entry /><entry>L+ L M+D + + +PLS+  ++LP+Y +IK  L EPS+VDME G+Y+ T + E</entry><entry /></row><row><entry>Sbjct:</entry><entry>304</entry><entry>LIRLTMNDSDEVLVPLSEMSKKLPYYSKIKPQLSEPSVVDMEAGIYSYTVADKLIMEVEE</entry><entry>363</entry></row><row><entry /></row><row><entry>Query:</entry><entry>330</entry><entry>DTKNKSTDKTQTQNGQVAENSQGQTNNSNTNQQGQQ</entry><entry>365</entry></row><row><entry /><entry /><entry>  K ++ +  + Q E  + Q SN NQ  Q+</entry><entry /></row><row><entry>Sbjct:</entry><entry>364</entry><entry>KAKQEAKEAEKKQE----EEQKKQEEESNRNQTTQR</entry><entry>395</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 217&gt; which encodes the amino acid sequence &lt;SEQ ID 218&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00234" num="00234"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.45</entry><entry>Transmembrane</entry><entry>106-122 (102-125)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4779(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00235" num="00235"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 152/381 (39%), Positives = 232/381 (59%), Gaps = 14/381 (3%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>KKSDTPEKEEVVLTEWQKRNLEFLKKRKEDEEEQKRINEKLRLDKRSKLNISSPEEP---</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>K  +    +++VLTEWQKRN+EFLKK+K+  EE+K++ EKL  DK+++    +  E</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>KDKEKQSDDKLVLTEWQKRNIEFLKKKKQQAEEEKKLKEKLLSDKKAQQQAQNASEAVEL</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>--QNTTKIKKLHFPKISRPKIEKK--QKKEKIVNSLAKTNRIRTAPIFVVAFLVILVSVF</entry><entry>116</entry></row><row><entry /><entry /><entry>     T  +++     S+PK  KK  Q KEK    +A     ++ P+ + A L++ VS+F</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>KTDEKTDSQEIESETTSKPKKTKKVRQPKEKSATQIAFQ---KSLPVLLGALLLMAVSIF</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>117</entry><entry>LLTPFSKQKTITVSGNQHTPDDILIEKTNIQKNDYFFSLIFKHKAIEQRLAAEDVWVKTA</entry><entry>176</entry></row><row><entry /><entry /><entry>++TP+SK+K  +V GN  T  D LI+ + ++ +DY+ +L+      E+ +     WVK+</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>MITPYSKKKEFSVRGNHQTNLDELIKASKVKASDYWLTLLTSPGQYERPILRTIPWVKSV</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>177</entry><entry>QMTYQFPNKFHIQVQENKIIAYAHTKQGYQPVLETGKKADPVNSSELPKHFLTINLDKED</entry><entry>236</entry></row><row><entry /><entry /><entry> ++YQFPN F   V E +IIAYA  + G+QP+LE GK+ D V +SELPK FL +NL  E</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>HLSYQFPNHFLFNVIEFEIIAYAQVENGFQPILENGKRVDKVRASELPKSFLILNLKDEK</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>237</entry><entry>SIKLLIKDLKALDPDLISEIQVISLADSKTTPDLLLLDMHDGNSIRIPLSRFKERLPFYK</entry><entry>296</entry></row><row><entry /><entry /><entry>+I+ L+K L  L   L+  I+ +SLA+SKTT DLLL++MHDGN +R+P S+   +LP+Y+</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>AIQQLVKQLTTLPKKLVKNIKSVSLANSKTTADLLLIEMHDGNVVRVPQSQLTLKLPYYQ</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>297</entry><entry>QIKKNLKEPSIVDMEVGVYTTTNTIESTPVKAEDTKNKSTDKTQTQNGQVAENSQGQTNN</entry><entry>356</entry></row><row><entry /><entry /><entry>++KKNL+  SIVDMEVG+YTTT  IE+ P      +  + DK   + G+     Q QT+N</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>KLKKNLENDSIVDMEVGIYTTTQEIENQPEVPLTPEQNAADKEGDKPGE----HQEQTDN</entry><entry>355</entry></row><row><entry /></row><row><entry>Query:</entry><entry>357</entry><entry>SNTNQQGQQIATEQAPNPQNV</entry><entry>377</entry></row><row><entry /><entry /><entry> +     Q    +  P+P+ V</entry></row><row><entry>Sbjct:</entry><entry>356</entry><entry>DSETPANQSSPQQTPPSPETV</entry><entry>376</entry></row></tbody></tgroup></table></tables>

SEQ ID 216 (GBS85) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 17</figref> (lane 10; MW 45.2 kDa).

The GBS85-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 105A</figref>; see also <figref idrefs="DRAWINGS">FIG. 193</figref>, lane 5) and used to immunise mice (lane 1 product; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 105B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 105C</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 68

A DNA sequence (GBSx0068) was identified in <i>S. agalactiae </i>&lt;SEQ ID 219&gt; which encodes the amino acid sequence &lt;SEQ ID 220&gt;. This protein is predicted to be cell division protein FtsA (ftsA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00236" num="00236"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.19</entry><entry>Transmembrane</entry><entry>322-338 (321-338)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2275(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00237" num="00237"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95439 GB:AF068901 cell division protein FtsA [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 292/457 (63%), Positives = 366/457 (79%), Gaps = 1/457 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MARNGFFTGLDIGTSSIKVLVAEFIANEMNVIGVSNVPSSGVKDGIIIDIEAAATAIKEA</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAR GFFTGLDIGTSS+KVLVAE    E+NVIGVSN  S GVKDGII+DI+AAATAIK A</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAREGFFTGLDIGTSSVKVLVAEQRNGELNVIGVSNAKSKGVKDGIIVDIDAAATAIKSA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VKQAEEKAGITIDKINVGLPANLLQIEPTQGMIPVPNESKEIKDEDVESVVKSALTKSIT</entry><entry>120</entry></row><row><entry /><entry /><entry>+ QAEEKAGI+I  +NVGLP NLLQ+EPTQGMIPV +++KEI D+DVE+VVKSALTKS+T</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ISQAEEKAGISIKSVNVGLPGNLLQVEPTQGMIPVTSDTKEITDQDVENVVKSALTKSMT</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>PEREVISLIPLEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPTTILHNLRKTVERAGIKV</entry><entry>180</entry></row><row><entry /><entry /><entry>P+REVI+ IP EFIVDGFQGIRDPRGMMG+RLEMRGL+YTGP TILHNLRKTVERAG++V</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PDREVITFIPLEFIVDGFQGIRDPRGMMGVRLEMRGLLYTGPRTILHNLRKTVERAGVQV</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>EHVVIAPLALAKSVLNEGEREFGATVIDMGGGQTTVASMRNQELQYTNIYSEGSDYVTKD</entry><entry>240</entry></row><row><entry /><entry /><entry>E+V+I+PLA+ +SVLNEGEREFGATVIDMG GQTTVA++RNQELQ+T+I  EG DYVTKD</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>ENVIISPLAMVQSVLNEGEREFGATVIDMGAGQTTVATIRNQELQFTHILQEGGDYVTKD</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>ISKVLRTTVEIAEALKFNFGQANVEEASTSDTVQVNVVGNEEPVEITESYLSQIISGRIR</entry><entry>300</entry></row><row><entry /><entry /><entry>ISKVL+T+ ++AE LK N+G+A    AS  +T QV V+G  E VE+TE+YLS+IIS RI+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>ISKVLKTSRKLAEGLKLNYGEAYPPLAS-KETFQVEVIGEVEAVEVTEAYLSEIISARIK</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>QILEHVKQDLGRGRLLDLPGGIILVGGGAIMPGVVEVAQQIFGTRVKLHVPNQVGIRNPM</entry><entry>360</entry></row><row><entry /><entry /><entry> ILE +KQ+L R RLLDLPGGI+L+GG AI+PG+VE+AQ++FG RVKL+VPNQVGIRNP</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>HILEQIKQELDRRRLLDLPGGIVLIGGNAILPGMVELAQEVFGVRVKLYVPNQVGIRNPA</entry><entry>359</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>FANVISIVDYVGMMSEVDIIAQHAVTGDEMLRHKPVDFDYKEKTNTMSTMPYSEPLTSSM</entry><entry>420</entry></row><row><entry /><entry /><entry>FA+VIS+ ++ G ++EV+++AQ A+ G+  L H+P+ F    +               +</entry></row><row><entry>Sbjct:</entry><entry>360</entry><entry>FAHVISLSEFAGQLTEVNLLAQGAIKGENDLSHQPISFGGMLQKTAQFVQSTPVQPAPAP</entry><entry>419</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>EDSNLEPIRARENAQEPTEPKANIGERIRGIFGSMFD</entry><entry>457</entry></row><row><entry /><entry /><entry>E   +P     + Q+ ++ K  + +R RG+ GSMFD</entry></row><row><entry>Sbjct:</entry><entry>420</entry><entry>EVEPVAPTEPMADFQQASQNKPKLADRFRGLIGSMFD</entry><entry>456</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 221&gt; which encodes the amino acid sequence &lt;SEQ ID 222&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00238" num="00238"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.35</entry><entry>Transmembrane</entry><entry>313-329 (312-329)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2338(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00239" num="00239"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95439 GB:AF068901 cell division protein FtsA [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 299/448 (66%), Positives = 368/448 (81%), Gaps = 4/448 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>LDIGTSSIKVLVAEFISGEMNVIGVSNVPSTGVKDGIIIDIEAAATAIKTAVEQAEEKAG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>LDIGTSS+KVLVAE  +GE+NVIGVSN  S GVKDGII+DI+AAATAIK+A+ QAEEKAG</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>LDIGTSSVKVLVAEQRNGELNVIGVSNAKSKGVKDGIIVDIDAAATAIKSAISQAEEKAG</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>MTIEKVNVGLPANLLQIEPTQGMIPVPSESKEIKDEDVDSVVKSALTKSITPERSVISLV</entry><entry>120</entry></row><row><entry /><entry /><entry>++I+ VNVGLP NLLQ+EPTQGMIPV S++KEI D+DV++VVKSALTKS+TP+REVI+ +</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>ISIKSVNVGLPGNLLQVEPTQGMIPVTSDTKEITDQDVENVVKSALTKSMTPDREVITFI</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>PEEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPSTILHNLRKTVERAGIKVENIIISPLA</entry><entry>180</entry></row><row><entry /><entry /><entry>PEEFIVDGFQGIRDPRGMMG+RLEMRGL+YTGP TILHNLRKTVERAG++VEN+IISPLA</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>PEEFIVDGFQGIRDPRGMMGVRLEMRGLLYTGPRTILHNLRKTVERAGVQVENVIISPLA</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>MAKTILNEGEREFGATVIDMGGGQTTVASMRAQELQYTNIYAEGGEYITKDISKVLKTSL</entry><entry>240</entry></row><row><entry /><entry /><entry>M +++LNEGEREFGATVIDMG GQTTVA++R QELQ+T+I  EGG+Y+TKDISKVLKTS</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>MVQSVLNEGEREFGATVIDMGAGQTTVATIRNQELQFTHILQEGGDYVTKDISKVLKTSR</entry><entry>249</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>AIAEALKFNFGQAEISEASITETVKVDVVGSEEPVEVTERYLSEIISARIRHILDRVKQD</entry><entry>300</entry></row><row><entry /><entry /><entry> +AE LK N+G+A    AS  ET +V+V+G  E VEVTE YLSEIISARI+HIL+++KQ+</entry></row><row><entry>Sbjct:</entry><entry>250</entry><entry>KLAEGLKLNYGEAYPPLAS-KETFQVEVIGEVEAVEVTEAYLSEIISARIKHILEQIKQE</entry><entry>308</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>LERGRLLDLPGGIVLIGGGAIMPGVVEIAQEIFGVTVKLHVPNQVGIRNPMFSNVISLVE</entry><entry>360</entry></row><row><entry /><entry /><entry>L+R RLLDLPGGIVLIGG AI+PG+VE+AQE+FGV VKL+VPNQVGIRNP F++VISL E</entry></row><row><entry>Sbjct:</entry><entry>309</entry><entry>LDRRRLLDLPGGIVLIGGNAILPGMVELAQEVFGVRVKLYVPNQVGIRNPAFAHVISLSE</entry><entry>368</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>YVGMMSEVDVLAQTAVSGEELLRRKPIDFSGQESYLPDYDDSRRPESTIGYEQQ---ASQ</entry><entry>417</entry></row><row><entry /><entry /><entry>+ G ++EV++LAQ A+ GE  L  +PI F G       +  S   +     E +    ++</entry></row><row><entry>Sbjct:</entry><entry>369</entry><entry>FAGQLTEVNLLAQGAIKGENDLSHQPISFGGMLQKTAQFVQSTPVQPAPAPEVEPVAPTE</entry><entry>428</entry></row><row><entry /></row><row><entry>Query:</entry><entry>418</entry><entry>TAYDSQVPSDPKQKISERVRGIFGSMFD</entry><entry>445</entry></row><row><entry /><entry /><entry>   D Q  S  K K+++R RG+ GSMFD</entry></row><row><entry>Sbjct:</entry><entry>429</entry><entry>PMADFQQASQNKPKLADRFRGLIGSMFD</entry><entry>456</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00240" num="00240"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 349/456 (76%), Positives = 402/456 (87%), Gaps = 19/456 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>10</entry><entry>LDIGTSSIKVLVAEFIANEMNVIGVSNVPSSGVKDGIIIDIEAAATAIKEAVKQAEEKAG</entry><entry>69</entry><entry /></row><row><entry /><entry /><entry>LDIGTSSIKVLVAEFI+ EMNVIGVSNVPS+GVKDGIIIDIEAAATAIK AV+QAEEKAG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LDIGTSSIKVLVAEFISGEMNVIGVSNVPSTGVKDGIIIDIEAAATAIKTAVEQAEEKAG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>70</entry><entry>ITIDKINVGLPANLLQIEPTQGMIPVPNESKEIKDEDVESVVKSALTKSITPEREVISLI</entry><entry>129</entry></row><row><entry /><entry /><entry>+TI+K+NVGLPANLLQIEPTQGMIPVP+ESKEIKDEDV+SVVKSALTKSITPEREVISL+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>MTIEKVNVGLPANLLQIEPTQGMIPVPSESKEIKDEDVDSVVKSALTKSITPEREVISLV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>130</entry><entry>PLEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPTTILHNLRKTVERAGIKVEHVVIAPLA</entry><entry>189</entry></row><row><entry /><entry /><entry>P EFIVDGFQGIRDPRGMMGIRLEMRGLIYTGP+TILHNLRKTVERAGIKVE+++I+PLA</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PEEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPSTILHNLRKTVERAGIKVENIIISPLA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>190</entry><entry>LAKSVLNEGEREFGATVIDMGGGQTTVASMRNQELQYTNIYSEGSDYVTKDISKVLRTTV</entry><entry>249</entry></row><row><entry /><entry /><entry>+AK++LNEGEREFGATVIDMGGGQTTVASMR QELQYTNIY+EG +Y+TKDISKVL+T++</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>MAKTILNEGEREFGATVIDMGGGQTTVASMRAQELQYTNIYAEGGEYITKDISKVLKTSL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>250</entry><entry>EIAEALKFNFGQANVEEASTSDTVQVNVVGNEEPVEITESYLSQIISGRIRQILEHVKQD</entry><entry>309</entry></row><row><entry /><entry /><entry> IAEALKFNFGQA + EAS ++TV+V+VVG+EEPVE+TE YLS+IIS RIR IL+ VKQD</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AIAEALKFNFGQAEISEASITETVKVDVVGSEEPVEVTERYLSEIISARIRHILDRVKQD</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>310</entry><entry>LGRGRLLDLPGGIILVGGGAIMPGVVEVAQQIFGTRVKLHVPNQVGIRNPMFANVISIVD</entry><entry>369</entry></row><row><entry /><entry /><entry>L RGRLLDLPGGI+L+GGGAIMPGVVE+AQ+IFG  VKLHVPNQVGIRNPMF+NVIS+V+</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LERGRLLDLPGGIVLIGGGAIMPGVVEIAQEIFGVTVKLHVPNQVGIRNPMFSNVISLVE</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>370</entry><entry>YVGMMSEVDIIAQHAVTGDEMLRHKPVDF--------DYKEKTNTMSTMPYSEPLTSSME</entry><entry>421</entry></row><row><entry /><entry /><entry>YVGMMSEVD++AQ AV+G+E+LR KP+DF        DY +     ST+ Y +  + +</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>YVGMMSEVDVLAQTAVSGEELLRRKPIDFSGQESYLPDYDDSRRPESTIGYEQQASQTAY</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>422</entry><entry>DSNLEPIRARENAQEPTEPKANIGERIRGIFGSMFD</entry><entry>457</entry></row><row><entry /><entry /><entry>DS           Q P++PK  I ER+RGIFGSMFD</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>DS-----------QVPSDPKQKISERVRGIFGSMFD</entry><entry>445</entry></row></tbody></tgroup></table></tables>

SEQ ID 220 (GBS73) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 17</figref> (lane 5; MW 47.8 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 20</figref> (lane 5; MW 70.1 kDa).

GBS73-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 197</figref>, lane 7.

The GBS73-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 103A</figref>) and used to immunise mice (lane 1 product; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 103B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 103C</figref>) and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 69

A DNA sequence (GBSx0069) was identified in <i>S. agalactiae </i>&lt;SEQ ID 223&gt; which encodes the amino acid sequence &lt;SEQ ID 224&gt;. This protein is predicted to be cell division protein FtsZ (ftsz). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00241" num="00241"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.97</entry><entry>Transmembrane</entry><entry>117-133 (117-133)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>\\\\\\\\\\\\\\\bacterial membrane --- Certainty = 0.1786 (Affirmative) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\\\bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00242" num="00242"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95440 GB:AF068901 cell division protein FtsZ [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 327/426 (76%), Positives = 363/426 (84%), Gaps = 7/426 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVFSFDTASVQGAVIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M FSFDTA+ QGAVIKVIGVGGGGGNAINRM+DEGV GVEFIAANTD+QALSS+KAETVI</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTFSFDTAAAQGAVIKVIGVGGGGGNAINRMVDEGVTGVEFIAANTDVQALSSTKAETVI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEEVLTEALTGADMVFITAGMGGGSGTGAAPVIAR</entry><entry>120</entry></row><row><entry /><entry /><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEE LTEA++GADMVFITAGMGGGSGTGAAPVIAR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEETLTEAISGADMVFITAGMGGGSGTGAAPVIAR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IAKSLGALTVAVITRPFGFEGNKRSNFAIEGIQELREQVDTLLIISNNNLLEIVDKKTPL</entry><entry>180</entry></row><row><entry /><entry /><entry>IAK LGALTV V+TRPFGFEG+KR  FA+EGI +LRE VDTLLIISNNNLLEIVDKKTPL</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IAKDLGALTVGVVTRPFGFEGSKRGQFAVEGINQLREHVDTLLIISNNNLLEIVDKKTPL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERITE</entry><entry>240</entry></row><row><entry /><entry /><entry>LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEER+ E</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERVVE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>AARKAIYSPLLETTIDGAEDVIVNVTGGMDMTLTEAEEASEIVSQAAGKGVNIWLGTSID</entry><entry>300</entry></row><row><entry /><entry /><entry>AARKAIYSPLLETTIDGAEDVIVNVTGG+D+TL EAEEAS+IV+QAAG+GVNIWLGTSID</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AARKAIYSPLLETTIDGAEDVIVNVTGGLDLTLIEAEEASQIVNQAAGQGVNIWLGTSID</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>MDMKDEIRVTVVATGVRKDKTNQVSGFTTSAPTNQAPSERQSTSNSNFDRRGNFDMTESR</entry><entry>360</entry></row><row><entry /><entry /><entry>  M+DEIRVTVVATGVR+D+  +V      + TN   + + + S+  FDR  +FDM E+</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>ESMRDEIRVTVVATGVRQDRVEKVVAPQARSATNYRETVKPAHSH-GFDR--HFDMAETA</entry><entry>357</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>ENPTQQNQPHAQNQQQSSAFGNWDLRRDNISRPTEGELDSKLSMSTFSENDDMDDELETP</entry><entry>420</entry></row><row><entry /><entry /><entry>E+P Q   P      Q+SAFG+WDLRR++I R T+  +            D  +DEL+TP</entry></row><row><entry>Sbjct:</entry><entry>358</entry><entry>ELPKQ--NPRRLEPTQASAFGDWDLRRESIVRTTDSVVSPVERFEAPISQD--EDELDTP</entry><entry>413</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>PFFKNR</entry><entry>426</entry></row><row><entry /><entry /><entry>PFFKNR</entry></row><row><entry>Sbjct:</entry><entry>414</entry><entry>PFFKNR</entry><entry>419</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 225&gt; which encodes the amino acid sequence &lt;SEQ ID 226&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00243" num="00243"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.81</entry><entry>Transmembrane</entry><entry>117-133 (117-133)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>\\\\\\\\\\\\\\\bacterial membrane --- Certainty = 0.1723 (Affirmative) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\\\bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00244" num="00244"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 372/439 (84%), Positives = 391/439 (88%), Gaps = 13/439 (2%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVFSFDTASVQGAVIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M FSFDTAS+QGA+IKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAFSFDTASIQGAIIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEEVLTEALTGADMVFITAGMGGGSGTGAAPVIAR</entry><entry>120</entry></row><row><entry /><entry /><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEE+LTEALTGADMVFITAGMGGGSGTGAAPVIAR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QLGPKLTRGLGAGGQPEVGRKAAEESEEILTEALTGADMVFITAGMGGGSGTGAAPVIAR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IAKSLGALTVAVITRPFGFEGNKRSNFAIEGIQELREQVDTLLIISNNNLLEIVDKKTPL</entry><entry>180</entry></row><row><entry /><entry /><entry>IAKSLGALTVAV+TRPFGFEGNKR NFAIEGI+ELREQVDTLLIISNNNLLEIVDKKTPL</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IAKSLGALTVAVVTRPFGFEGNKRGNFAIEGIEELREQVDTLLIISNNNLLEIVDKKTPL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERITE</entry><entry>240</entry></row><row><entry /><entry /><entry>LEALSEADNVLRQGVQGITDLIT+PGLINLDFADVKTVMANKGNALMGIGIGSGEERI E</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LEALSEADNVLRQGVQGITDLITSPGLINLDFADVKTVMANKGNALMGIGIGSGEERIVE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>AARKAIYSPLLETTIDGAEDVIVNVTGGMDMTLTEAEEASEIVSQAAGKGVNIWLGTSID</entry><entry>300</entry></row><row><entry /><entry /><entry>AARKAIYSPLLETTIDGA+DVIVNVTGG+DMTLTEAEEASEIV QAAG+GVNIWLGTSID</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AARKAIYSPLLETTIDGAQDVIVNVTGGLDMTLTEAEEASEIVGQAAGQGVNIWLGTSID</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>MDMKDEIRVTVVATGVRKDKTNQVSGF---TTSAPTN--------QAPSERQSTSNSNFD</entry><entry>349</entry></row><row><entry /><entry /><entry>  MKD+IRVTVVATGVR++K  QVSGF    T   TN         A  + + +    FD</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>DTMKDDIRVTVVATGVRQEKAEQVSGFRQPRTFTQTNAQQVAGAQYASDQAKQSVQPGFD</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>350</entry><entry>RRGN--FDMTESREMPTQQNQPHAQNQQQSSAFGNWDLRRDNISRPTEGELDSKLSMSTF</entry><entry>407</entry></row><row><entry /><entry /><entry>RR N  FDM ESRE+P+ Q      NQ Q SAFGNWDLRRDNISRPTEGELD+ L+MSTF</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>RRSNFDFDMGESREIPSAQKVISNHNQNQGSAFGNWDLRRDNISRPTEGELDNHLNMSTF</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>408</entry><entry>SENDDMDDELETPPFFKNR</entry><entry>426</entry></row><row><entry /><entry /><entry>S NDD DDELETPPFFKNR</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>SANDDSDDELETPPFFKNR</entry><entry>439</entry></row></tbody></tgroup></table></tables>

SEQ ID 224 (GBS163) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 28</figref> (lane 7; MW 44 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 34</figref> (lane 4; MW 69 kDa).

The GBS163-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 114A</figref>; see also <figref idrefs="DRAWINGS">FIG. 198</figref>, lane 11) and used to immunise mice (lane 1 product; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 114B</figref>), FACS and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 70

A DNA sequence (GBSx0070) was identified in <i>S. agalactiae </i>&lt;SEQ ID 227&gt; which encodes the amino acid sequence &lt;SEQ ID 228&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00245" num="00245"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>\\\\\\\\\\\\\\bacterial cytoplasm --- Certainty = 0.2750 (Affirmative) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\\bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>\\\\\\\\\\\\\\\\bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00246" num="00246"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95441 GB:AF068901 YlmE [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 140/223 (62%), Positives = 177/223 (78%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>MNLQENKTAIFDNVSKLALKAGRAHESVHIVAVTKYVNCQTTEALIRTGVNHIGENRVDK</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>MN++EN   +F  V++ +L A R   SV ++AVTKYV+  T EAL+  GV+HIGENRVDK</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNVKENTELVFREVAEASLSAHRESGSVSVIAVTKYVDVPTAEALLPLGVHHIGENRVDK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>FLEKYQALKDEKLTWHLIGSLQRRKVKDVINYVDYFHALDSVKLAAEIQKHAQKLIKCFL</entry><entry>121</entry></row><row><entry /><entry /><entry>FLEKY+ALKD  +TWHLIG+LQRRKVKDVI YVDYFHALDSVKLA EIQK + ++IKCFL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FLEKYEALKDRDVTWHLIGTLQRRKVKDVIQYVDYFHALDSVKLAGEIQKRSDRVIKCFL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>QVNISREDSKHGFTIEQIDDALNLISRYDKIELIGIMTMAPLKATKEEISSIFEETESLR</entry><entry>181</entry></row><row><entry /><entry /><entry>QVNIS+E+SKHGF+ E++ + L  ++R DKIE +G+MTMAP +A+ E++  IF+  + L+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>QVNISKEESKHGFSREELLEILPELARLDKIEYVGLMTMAPFEASSEQLKEIFKAAQDLQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>KRLQARNIERMPFTELSMGMSRDYDIAIQNGSTFVRIGTSFFK</entry><entry>224</entry></row><row><entry /><entry /><entry>+ +Q + I  MP TELSMGMSRDY  AIQ GSTFVRIGTSFFK</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>REIQEKQIPNMPMTELSMGMSRDYKEAIQFGSTFVRIGTSFFK</entry><entry>223</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 229&gt; which encodes the amino acid sequence &lt;SEQ ID 230&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00247" num="00247"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2451(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00248" num="00248"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 133/222 (59%), Positives = 164/222 (72%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>MNLQENKTAIFDNVSKLALKAGRAHESVHIVAVTKYVNCQTTEALIRTGVNHIGENRVDK</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>M+L  NK  IF+ +      A R ++SV ++AVTKYV+      LI  G+ HI ENRVDK</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MDLLTNKKKIFETIRLSTEAANRTNDSVSVIAVTKYVDSTIAGQLIEAGIEHIAENRVDK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>FLEKYQALKDEKLTWHLIGSLQRRKVKDVINYVDYFHALDSVKLAAEIQKHAQKLIKCFL</entry><entry>121</entry></row><row><entry /><entry /><entry>FLEKY ALK   + WHLIG+LQRRKVK+VINYVDYFHALDSV+LA EI K A   +KCFL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FLEKYDALKYMPVKWHLIGTLQRRKVKEVINYVDYFHALDSVRLALEINKRADHPVKCFL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>QVNISREDSKHGFTIEQIDDALNLISRYDKIELIGIMTMAPLKATKEEISSIFEETESLR</entry><entry>181</entry></row><row><entry /><entry /><entry>QVNIS+E+SKHGF I +ID+A+  I + +KI+L+G+MTMAP  A+KE I +IF +   LR</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>QVNISKEESKHGFNISEIDEAIGEIGKMEKIQLVGLMTMAPANASKESIITIFRQANQLR</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>KRLQARNIERMPFTELSMGMSRDYDIAIQNGSTFVRIGTSFF</entry><entry>223</entry></row><row><entry /><entry /><entry>K LQ +  + MPFTELSMGMS DY IAIQ GSTF+RIG +FF</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KNLQLKKRKNMPFTELSMGMSNDYPIAIQEGSTFIRIGRAEF</entry><entry>222</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 71

A DNA sequence (GBSx0071) was identified in <i>S. agalactiae </i>&lt;SEQ ID 231&gt; which encodes the amino acid sequence &lt;SEQ ID 232&gt;. This protein is predicted to be YlmF. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00249" num="00249"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2194(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9617&gt; which encodes amino acid sequence &lt;SEQ ID 9618&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00250" num="00250"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC95442 GB:AF068901 YlmF [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 86/200 (43%), Positives = 120/200 (60%), Gaps = 25/200 (12%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MALKDRFDKIISYFDTDDVSENEVHEVQERTSVQRDSRAATAQEASQRSHMTNSASEEMI</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>M+LKDRFD+ I YF T+D   +  +E       +RD    T+  +SQ   +  +   +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSLKDRFDRFIDYF-TEDEDSSLPYE-------KRDEPVFTSVNSSQEPALPMNQPSQSA</entry><entry>52</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>GSRPRTYTYDPNRQERQRVQRDNAYQQATPRVQNKDSVRQQREQVTIALKYPRKYEDAQE</entry><entry>124</entry></row><row><entry /><entry /><entry>G++    T    RQ+    +  N  Q+AT             ++V I ++YPRKYEDA E</entry></row><row><entry>Sbjct:</entry><entry>53</entry><entry>GTKENNITRLHARQQ----ELANQSQRAT-------------DKVIIDVRYPRKYEDATE</entry><entry>95</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>IVDLLIVNECVLIDFQYMLDAQARRCLDYIDGASRVLYGSLQKVGSSMFLLTPANVMVDI</entry><entry>184</entry></row><row><entry /><entry /><entry>IVDLL  NE +LIDFQYM + QARRCLDY+DGA  VL G+L+KV S+M+LLTP NV+V++</entry></row><row><entry>Sbjct:</entry><entry>96</entry><entry>IVDLLAGNESILIDFQYMTEVQARRCLDYLDGACHVLAGNLKKVASTMYLLTPVNVIVNV</entry><entry>155</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>EEMNIPKTGQETSFDFDMKR</entry><entry>204</entry></row><row><entry /><entry /><entry>E++ +P   Q+  F FDMKR</entry></row><row><entry>Sbjct:</entry><entry>156</entry><entry>EDIRLPDEDQQGEFGFDMKR</entry><entry>175</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 233&gt; which encodes the amino acid sequence &lt;SEQ ID 234&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00251" num="00251"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.64</entry><entry>Transmembrane</entry><entry>142-158 (142-158)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1256(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00252" num="00252"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95442 GB: AF068901 YlmF [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 82/219 (37%), Positives = 113/219 (51%), Gaps = 46/219 (21%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MAFKDTFNKMISYFDTDEVNEVEEDVAASTDNVIP--RSQQSVRASSHPKQEPRNNHVQQ</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>M+ KD F++ I YF  DE            D+ +P  +  + V  S +  QEP     Q</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSLKDRFDRFIDYFTEDE------------DSSLPYEKRDEPVFTSVNSSQEPALPMNQP</entry><entry>48</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>DHQARSQEQTRSQMHPKHGTSERYYQQSQPKEGHEMVDRRKRMSTSSIANRREQYQQSTC</entry><entry>122</entry></row><row><entry /><entry /><entry>   A ++E   +++H +                              +AN     Q</entry></row><row><entry>Sbjct:</entry><entry>49</entry><entry>SQSAGTKENNITRLHARQ---------------------------QELAN-----QSQRA</entry><entry>76</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>SDQTTIALKYPRKYEDAQEIVDLLIVNECVLIDFQFMLDAQARRCLDFIDGASKVLYGSL</entry><entry>182</entry></row><row><entry /><entry /><entry>+D+  I ++YPRKYEDA EIVDLL  NE +LIDFQ+M + QARRCLD++DGA  VL G+L</entry></row><row><entry>Sbjct:</entry><entry>77</entry><entry>TDKVIIDVRYPRKYEDATEIVDLLAGNESILIDFQYMTEVQARRCLDYLDGACHVLAGNL</entry><entry>136</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>QKVGSSMYLLAPSNVSVNIEEMTIPHTTQDIGFDFDMKR</entry><entry>221</entry></row><row><entry /><entry /><entry>+KV S+MYLL P NV VN+E++ +P   Q   F FDMKR</entry></row><row><entry>Sbjct:</entry><entry>137</entry><entry>KKVASTMYLLTPVNVIVNVEDIRLPDEDQQGEFGFDMKR</entry><entry>175</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00253" num="00253"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 118/222 (53%), Positives = 145/222 (65%), Gaps = 17/222 (7%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEGNMALKDRFDKIISYFDTDDVSENEVHEVQERTSV----QRDSRAATAQEAS------</entry><entry>50</entry><entry /></row><row><entry /><entry /><entry>ME  MA KD F+K+ISYFDTD+V+E E        +V    Q+  RA++  +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MENKMAFKDTFNKMISYFDTDEVNEVEEDVAASTDNVIPRSQQSVRASSHPKQEPRNNHV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>51</entry><entry>QRSHMTNSAEEEMIGSRPRTYTYDPNRQERQRVQR----DNAYQQATPRVQNKDSVRQQR</entry><entry>106</entry></row><row><entry /><entry /><entry>Q+ H   S E+      P+  T +   Q+ Q  +     D   + +T  + N+    QQ</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QQDHQARSQEQTRSQMHPKHGTSERYYQQSQPKEGHEMVDRRKRMSTSSIANRREQYQQS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>107</entry><entry>---EQVTIALKYPRKYEDAQEIVDLLIVNECVLIDFQYMLDAQARRCLDYIDGASRVLYG</entry><entry>163</entry></row><row><entry /><entry /><entry>   +Q TIALKYPRKYEDAQEIVDLLIVNECVLIDFQ+MLDAQARRCLD+IDGAS+VLYG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TCSDQTTIALKYPRKYEDAQEIVDLLIVNECVLIDFQFMLDAQARRCLDFIDGASKVLYG</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>164</entry><entry>SLQKVGSSMFLLTPANVMVDIEEMNIPKTGQETSFDFDMKRR</entry><entry>205</entry></row><row><entry /><entry /><entry>SLQKVGSSM+LL P+NV V+IEEM IP T Q+  FDFDMKRR</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SLQKVGSSMYLLAPSNVSVNIEEMTIPHTTQDIGFDFDMKRR</entry><entry>222</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 72

A DNA sequence (GBSx0072) was identified in <i>S. agalactiae </i>&lt;SEQ ID 235&gt; which encodes the amino acid sequence &lt;SEQ ID 236&gt;. This protein is predicted to be YlmH. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00254" num="00254"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3956(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00255" num="00255"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95444 GB: AF068901 YlmH [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 101/255 (39%), Positives = 161/255 (62%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>IYQHFRPEEYAFIHKIDHLAQYVENTYSFITTEFLNPREFKILESVLERRGSHYYTSGQY</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>IYQHF  E+  F+ K     + VE++Y+   T F+NP + K+L+ + +  G    +SG++</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>IYQHFSIEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTYGLACSSSGEF</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>FQTEYVKVIIAPEYYQLDMADFNLSLIEIKYNAKFNHLTHAKIMGTLLNYLGVKRSILGD</entry><entry>125</entry></row><row><entry /><entry /><entry>  +EYV+V++ P+Y+Q + +DF +SL EI Y+ KF HLTHAKI+GT++N LG++R + GD</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>VSSEYVRVLLYPDYFQPEFSDFEISLQEIVYSNKFEHLTHAKILGTVINQLGIERKLFGD</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>ILVEEGCAQVLVDSQMTNHLVHSVTKIGTASVQLAEVPLSKLLTPKQDIQKLTVIASSLR</entry><entry>185</entry></row><row><entry /><entry /><entry>ILV+E  AQ++++ Q        + KIG   V L E P ++ +   +  ++L +  SS R</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>ILVDEERAQIMINQQFLLLFQDGLKKIGRIPVSLEERPFTEKIDKLEQYRELDLSVSSFR</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>LDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLISVRGYGRFTLNHNLG</entry><entry>245</entry></row><row><entry /><entry /><entry>LD +L+ +LK+SR Q+ +LIE   V+VNY  V++    +  GDLISVR +GR  L  + G</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>LDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISVRKFGRLRLLQDKG</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>LTKNQKYKLEVDKMI</entry><entry>260</entry></row><row><entry /><entry /><entry> TK +K K+ V  ++</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>QTKKEKKKITVQLLL</entry><entry>259</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 237&gt; which encodes the amino acid sequence &lt;SEQ ID 238&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00256" num="00256"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.69</entry><entry>Transmembrane</entry><entry>46-62 (46-62)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1277(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00257" num="00257"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95444 GB: AF068901 YlmH [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 110/257 (42%), Positives = 161/257 (61%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>IYQHFHQEEYPFIDRMSDMINRVEDYYLLEVTEFLNPREVMILKSLIALTDLKMFVSTDY</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>IYQHF  E+ PF+D+  + I +VED Y   +T F+NP +  +LK L     L    S ++</entry><entry /></row><row><entry>Sbjct:</entry><entry>5</entry><entry>IYQHFSIEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTYGLACSSSGEF</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>YPSEYGRVIIAPGYYDLEQSDFQIALVEISYQAKFNQLTHSQILGTLINELGVKRNLFGD</entry><entry>126</entry></row><row><entry /><entry /><entry>  SEY RV++ P Y+  E SDF+I+L EI Y  KF  LTH++ILGT+IN+LG++R LFGD</entry><entry /></row><row><entry>Sbjct:</entry><entry>65</entry><entry>VSSEYVRVLLYPDYFQPEFSDFEISLQEIVYSNKFEHLTHAKILGTVINQLGIERKLFGD</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>VFVEMGYAQLMIKRELLDYFLGTITKIAKTSVKLREVNFDQLIRSIDNSQTLDILVSSFR</entry><entry>186</entry></row><row><entry /><entry /><entry>+ V+   AQ+MI ++ L  F   + KI +  V L E  F + I  ++  + LD+ VSSFR</entry><entry /></row><row><entry>Sbjct:</entry><entry>125</entry><entry>ILVDEERAQIMINQQFLLLFQDGLKKIGRIPVSLEERPFTEKIDKLEQYRELDLSVSSFR</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>LDGVVATILKKSRTQVIALIEANKIKVNYRVANKASDNLVIGDMVSIRGHGRFTLLADNG</entry><entry>246</entry></row><row><entry /><entry /><entry>LD +++ +LK SR Q   LIE   ++VNY V +K+   + +GD++S+R  GR  LL D G</entry><entry /></row><row><entry>Sbjct:</entry><entry>185</entry><entry>LDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISVRKFGRLRLLQDKG</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>247</entry><entry>VTKHGKQKITLSKMIHK</entry><entry>263</entry></row><row><entry /><entry /><entry> TK  K+KIT+  ++ K</entry><entry /></row><row><entry>Sbjct:</entry><entry>245</entry><entry>QTKKEKKKITVQLLLSK</entry><entry>261</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00258" num="00258"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 123/256 (48%), Positives = 177/256 (69%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>IYQHFRPEEYAFIHKIDHLAQYVENTYSFITTEFLNPREFKILESVLERRGSHYYTSGQY</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>IYQHF  EEY FI ++  +   VE+ Y    TEFLNPRE  IL+S++       + S  Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>7</entry><entry>IYQHFHQEEYPFIDRMSDMINRVEDYYLLEVTEFLNPREVMILKSLIALTDLKMFVSTDY</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>FQTEYVKVIIAPEYYQLDMADFNLSLIEIKYNAKFNHLTHAKIMGTLLNYLGVKRSILGD</entry><entry>125</entry></row><row><entry /><entry /><entry>+ +EY +VIIAP YY L+ +DF ++L+EI Y AKFN LTH++I+GTL+N LGVKR++ GD</entry><entry /></row><row><entry>Sbjct:</entry><entry>67</entry><entry>YPSEYGRVIIAPGYYDLEQSDFQIALVEISYQAKFNQLTHSQILGTLINELGVKRNLFGD</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>ILVEEGCAQVLVDSQMTNHLVHSVTKIGTASVQLAEVPLSKLLTPKQDIQKLTVIASSLR</entry><entry>185</entry></row><row><entry /><entry /><entry>+ VE G AQ+++  ++ ++ + ++TKI   SV+L EV   +L+    + Q L ++ SS R</entry><entry /></row><row><entry>Sbjct:</entry><entry>127</entry><entry>VFVEMGYAQLMIKRELLDYFLGTITKIAKTSVKLREVNFDQLIRSIDNSQTLDILVSSFR</entry><entry>186</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>LDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLISVRGYGRFTLNHNLG</entry><entry>245</entry></row><row><entry /><entry /><entry>LD ++ATILK SRTQ   LIEA+K+KVNY   N+ S+ LV GD++S+RG+GRFTL  + G</entry><entry /></row><row><entry>Sbjct:</entry><entry>187</entry><entry>LDGVVATILKKSRTQVIALIEANKIKVNYRVANKASDNLVIGDMVSIRGHGRFTLLADNG</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>LTKNQKYKLEVDKMIH</entry><entry>261</entry></row><row><entry /><entry /><entry>+TK+ K K+ + KMIH</entry><entry /></row><row><entry>Sbjct:</entry><entry>247</entry><entry>VTKHGKQKITLSKMIH</entry><entry>262</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 73

A DNA sequence (GBSx0073) was identified in <i>S. agalactiae </i>&lt;SEQ ID 239&gt; which encodes the amino acid sequence &lt;SEQ ID 240&gt;. This protein is predicted to be cell division protein DivIVA (septumplacement). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00259" num="00259"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5418 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00260" num="00260"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="350pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95445 GB: AF068901 cell division protein DivIVA [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 132/227 (58%), Positives = 179/227 (78%), Gaps = 2/227 (0%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="49pt" align="char" char="." /><colspec colname="5" colwidth="91pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MPLTALEIKDKTFSSKFRGYSEEEVNEFLEIVVDDYEDLIRRNREQEQYIKDLEEKIAYF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MP+T+LEIKDKTF ++FRG+  EEV+EFL+IVV DYEDL+R N ++   IK LEE+++YF</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MPITSLEIKDKTFGTRFRGFDPEEVDEFLDIVVRDYEDLVRANHDKNLRIKSLEERLSYF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NEMKESLSQSVILAQETAERVKISAQDEASNLMGKATFDAQHLIDEAKLKANQILRDATD</entry><entry>120</entry></row><row><entry /><entry /><entry>+E+K+SLSQSV++AQ+TAERVK +A + ++N++ +A  DAQ L++EAK KAN+ILR ATD</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DEIKDSLSQSVLIAQDTAERVKQAAHERSNNIIHQAEQDAQRLLEEAKYKANEILRQATD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DAKRVAIETEDLKRQSRVFHQRLLSELEGQLKLANSSAWEELLKPTAIYLQNSDASFKEV</entry><entry>180</entry></row><row><entry /><entry /><entry>+AK+VA+ETE+LK +SRVFHQRL S +E QL +  SS WE++L+PTA YLQ SD +FKEV</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NAKKVAVETEELKNKSRVFHQRLKSTIESQLAIVESSDWEDILRPTATYLQTSDEAFKEV</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>VEKVLDEDDALPVVDDTESFDATRQFSPDEMEELQRRVEESNKQLEE</entry><entry>227</entry></row><row><entry /><entry /><entry>V +VL E    P+  + E  D TRQFS  EM ELQ R+E ++K+L E</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VSEVLGEPIPAPI--EEEPIDMTRQFSQAEMAELQARIEVADKELSE</entry><entry>225</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 241&gt; which encodes the amino acid sequence &lt;SEQ ID 242&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00261" num="00261"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.6272 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00262" num="00262"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 180/254 (70%), Positives = 217/254 (84%), Gaps = 2/254 (0%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MPLTALEIKDKTFSSKFRGYSEEEVNEFLEIVVDDYEDLIRRNREQEQYIKDLEEKIAYF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M LT LEIKDKTF +KFRGY EEEVNEFL+IVVDDYE L+R+NR+ E  IKDLEEK++YF</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MALTTLEIKDKTFKTKFRGYCEEEVNEFLDIVVDDYEALVRKNRDNEARIKDLEEKLSYF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NEMKESLSQSVILAQETAERVKISAQDEASNLMGKATFDAQHLIDEAKLKANQILRDATD</entry><entry>120</entry></row><row><entry /><entry /><entry>+EMKESLSQSVILAQETAE+VK +A  EA+NL+ KAT+DAQHL+DE+K KANQ+LRDATD</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DEMKESLSQSVILAQETAEKVKATANAEATNLVSKATYDAQHLLDESKAKANQMLRDATD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DAKRVAIETEDLKRQSRVFHQRLLSELEGQLKLANSSAWEELLKPTAIYLQNSDASFKEV</entry><entry>180</entry></row><row><entry /><entry /><entry>+AKRVAIETE+LKRQ+RVFHQRL+S +E QL L+NS  W+ELL+PTAIYLQNSD +FKEV</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>EAKRVAIETEELKRQTRVFHQRLISSIESQLSLSNSPEWDELLQPTAIYLQNSDDAFKEV</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>VEKVLDEDDALPVVDDTESFDATRQFSPDEMEELQRRVEESNKQLEESGLLDTNNFQMEE</entry><entry>240</entry></row><row><entry /><entry /><entry>V+ VL+ED  +P  DD+ SFDATRQF+P+E+EELQRRV+ESNK+LE   L   ++   E</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VKTVLNED--IPESDDSASFDATRQFTPEELEELQRRVDESNKELEAYQLDSQSDSTTEP</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>PINLGETQTFKLNI</entry><entry>254</entry></row><row><entry /><entry /><entry> +NL ETQTFKLNI</entry><entry /></row><row><entry>Sbjct:</entry><entry>239</entry><entry>EVNLSETQTFKLNI</entry><entry>252</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 74

A DNA sequence (GBSx0074) was identified in <i>S. agalactiae </i>&lt;SEQ ID 243&gt; which encodes the amino acid sequence &lt;SEQ ID 244&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00263" num="00263"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><colspec colname="6" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −0.43</entry><entry>Transmembrane</entry><entry>841-857 (841-857)</entry><entry /><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.1171 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>             bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00264" num="00264"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC95446 GB: AF068901 isoleucine-tRNA synthetase [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 730/929 (78%), Positives = 822/929 (87%), Gaps = 1/929 (0%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="42pt" align="char" char="." /><colspec colname="5" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKLKETLNLGQTAFPMRAGLPNKEPQWQEAWDQADIYKKRQALNEGKPAFHLHDGPPYAN</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKLK+TLNLG+T FPMRAGLP KEP WQ+ W+ A +Y++RQ LN+GKP F LHDGPPYAN</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKLKDTLNLGKTEFPMRAGLPTKEPVWQKEWEDAKLYQRRQELNQGKPHFTLHDGPPYAN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GNIHVGHALNKISKDIIVRSKSMSGFRAPYVPGWDTHGLPIEQVLAKKGVKRKEMDLAEY</entry><entry>120</entry></row><row><entry /><entry /><entry>GNIHVGHA+NKISKDIIVRSKSMSGF AP++PGWDTHGLPIEQVL+K+GVKRKEMDL EY</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GNIHVGHAMNKISKDIIVRSKSMSGFYAPFIPGWDTHGLPIEQVLSRQGVKRKEMDLVEY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>LEMCRDYALSQVDKQRDDFKRLGVSADWENPYITLTPDYEADQVRVFGAMADKGYIYRGA</entry><entry>180</entry></row><row><entry /><entry /><entry>L++CR+YALSQVDKQR+DFKRLGVS DWENPY+TLTPDYEA Q+RVFG MA+KGYIYRGA</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LKLCREYALSQVDKQREDFKRLGVSGDWENPYVTLTPDYEAAQIRVFGEMANKGYIYRGA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTDTYIVVWTTTPFTVTAS</entry><entry>240</entry></row><row><entry /><entry /><entry>KPVYWSWSSESALAEAEIEYHD+ STSLYYANKVKDGKG+LDTDTYIVVWTTTPFT+TAS</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KPVYWSWSSESALAEAEIEYHDLVSTSLYYANKVKDGKGVLDTDTYIVVWTTTPFTITAS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>RGLTVGPDMEYVVVVPVGSERKYLLAEVLVDSLAAKFGWENFEIVTHHTGKELNHIVTEH</entry><entry>300</entry></row><row><entry /><entry /><entry>RGLTVG D++YV+V PVG  RK+++A  L+ SL+ KFGW + +++  + G+ELNHIVTEH</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>RGLTVGADIDYVLVQPVGEARKFVVAAELLTSLSEKFGWADVQVLETYRGQELNHIVTEH</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>PWDTEVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANGLDVVVTVDSRGLMMENA</entry><entry>360</entry></row><row><entry /><entry /><entry>PWDT VEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIAN L+V VTVD RG+MM+NA</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>PWDTAVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANNLEVAVTVDERGIMMKNA</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>GPDFEGQFYDKVTPLVKEKLGDLLLASEVINHSYPFDWRTKKPIIWRAVPQWFASVSKFR</entry><entry>420</entry></row><row><entry /><entry /><entry>GP+FEGQFY+KV P V EKLG+LLLA E I+HSYPFDWRTKKPIIWRAVPQWFASVSKFR</entry><entry /></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GPEFEGQFYEKVVPTVIEKLGNLLLAQEEISHSYPFDWRTKKPIIWRAVPQWFASVSKFR</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>QEILDEIEKTNFQPEWGKKRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT</entry><entry>480</entry></row><row><entry /><entry /><entry>QEILDETEK  F  EWGK RLYNMIRDRGDWVISRQR WGVPLPIFYAEDGTAIM  E</entry><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>QEILDEIEKVKFHSEWGKVRLYNMIRDRGDWVISRQRTWGVPLPIFYAEDGTAIMVAETI</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>DHVADLFAEYGSIVWWQRDAKDLLPAGYTHPGSPNGLFEKETDIMDVWFDSGSSWNGVMN</entry><entry>540</entry></row><row><entry /><entry /><entry>+HVA LF ++GS +WW+RDAKDLLP G+THPGSPNG F+KETDIMDVWFDSGSSWNGV+</entry><entry /></row><row><entry>Sbjct:</entry><entry>481</entry><entry>EHVAQLFSKHGSSIWWERDAKDLLPEGFTHPGSPNGEFKKETDIMDVWFDSGSSWNGVVV</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>ARENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAVLSQGFVLDGKGEKMSKSL</entry><entry>600</entry></row><row><entry /><entry /><entry> R  L+YPADLYLEGSDQYRGWFNSSLITSVA +G APYK +LSQGF LDGKGEKMSKSL</entry><entry /></row><row><entry>Sbjct:</entry><entry>541</entry><entry>NRPELTYPADLYLEGSDQYRGWFNSSLITSVANHGVAPYKQILSQGFALDGKGEKMSKSL</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>GNTILPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILEQTSETYRKIRNTLRFLIANTS</entry><entry>660</entry></row><row><entry /><entry /><entry>GNTI PSDVEKQFGAEILRLWVTSVDSSNDVRISMDIL Q SETYRKIRNTLRFLIANTS</entry><entry /></row><row><entry>Sbjct:</entry><entry>601</entry><entry>GNTIAPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILSQVSETYRKIRNTLRFLIANTS</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>661</entry><entry>DFNPKQDAVAYENLGAVDRYMTIKFNQVVDTINKAYAAYDFMAIYKAVVNFVTVDLSAFY</entry><entry>720</entry></row><row><entry /><entry /><entry>DFNP QD VAY+ L +VD+YMTI+FNQ+V TI  AYA ++F+ IYKA+VNF+ VDLSAFY</entry><entry /></row><row><entry>Sbjct:</entry><entry>661</entry><entry>DFNPAQDTVAYDELRSVDKYMTIRFNQLVKTIRDAYADFEFLTIYKALVNFINVDLSAFY</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>721</entry><entry>LDFAKDVVYIEAANSPERRPMQTVFYDILVKLTKLLTPILPHTAEEIWSYLEHEEEEFVQ</entry><entry>780</entry></row><row><entry /><entry /><entry>LDFAKDVVYIE A S ERR+MQTVFYDILVK+TKLLTPILPHTAEEIWSYLE E E+FVQ</entry><entry /></row><row><entry>Sbjct:</entry><entry>721</entry><entry>LDFAKDVVYIEGAKSLERRQMQTVFYDILVKITKLLTPILPHTAEEIWSYLEFETEDFVQ</entry><entry>780</entry></row><row><entry /></row><row><entry>Query:</entry><entry>781</entry><entry>LAEMPVAQTFSGQEEILEEWSAFMTLRTQAQKALEEARNAKVIGKSLEAHLTIYASQEVK</entry><entry>840</entry></row><row><entry /><entry /><entry>L+E+P  QTF+ QEEIL+ W+AFM  R QAQKALEEARNAKVIGKSLEAHLT+Y ++ VK</entry><entry /></row><row><entry>Sbjct:</entry><entry>781</entry><entry>LSELPEVQTFANQEEILDTWAAFMDFRGQAQKALEEARNAKVIGKSLEAHLTVYPNEVVK</entry><entry>840</entry></row><row><entry /></row><row><entry>Query:</entry><entry>841</entry><entry>TLLTALNSDIALLMIVSQLTIADEADKPADSVSFEGVAFTVEHAEGEVCERSRRIDPTTK</entry><entry>900</entry></row><row><entry /><entry /><entry>TLL A+NS++A L+IVS+LTIA+E   P  +SFE VAFTVE A GEVC+R RRIDPTT</entry><entry /></row><row><entry>Sbjct:</entry><entry>841</entry><entry>TLLEAVNSNVAQLLIVSELTIAEE-PAPEAALSFEDVAFTVERAAGEVCDRCRRIDPTTA</entry><entry>899</entry></row><row><entry /></row><row><entry>Query:</entry><entry>901</entry><entry>MRSYGVAVCDASAAIIEQYYPEAVAQGFE</entry><entry>929</entry></row><row><entry /><entry /><entry> RSY   +CD  A+I+E+ + +AVA+GFE</entry><entry /></row><row><entry>Sbjct:</entry><entry>900</entry><entry>ERSYQAVICDHCASIVEENFADAVAEGFE</entry><entry>928</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 245&gt; which encodes the amino acid sequence &lt;SEQ ID 246&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00265" num="00265"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><colspec colname="6" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −1.70</entry><entry>Transmembrame</entry><entry>849-865 (848-867)</entry><entry /><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.1680 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>             bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00266" num="00266"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 798/929 (85%), Positives = 857/929 (91%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKLKETLNLGQTAFPMRAGLPNKEPQWQEAWDQADIYKKRQALNEGKPAFHLHDGPPYAN</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKLKETLNLG+TAFPMRAGLPNKEPQWQ AW+QA++YKKRQ LN GKPAFHLHDGPPYAN</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKLKETLNLGKTAFPMRAGLPNKEPQWQAAWEQAELYKKRQELNAGKPAFHLHDGPPYAN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GNIHVGHALNKISKDIIVRSKSMSGFRAPYVPGWDTHGLPIEQVLAKKGVKRKEMDLAEY</entry><entry>120</entry></row><row><entry /><entry /><entry>GNIHVGHALNKISKDIIVRSKSMSGF+APYVPGWDTHGLPIEQVLAK+G+KRKEMDLAEY</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GNIHVGHALNKISKDIIVRSKSMSGFQAPYVPGWDTHGLPIEQVLAKQGIKRKEMDLAEY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>LEMCRDYALSQVDKQRDDFKRLGVSADWENPYITLTPDYEADQVRVFGAMADKGYIYRGA</entry><entry>180</entry></row><row><entry /><entry /><entry>LEMCR YALSQVDKQRDDFKRLGVSADWENPY+TL P +EADQ+RVFGAMA+KGYIYRGA</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LEMCRQYALSQVDKQRDDFKRLGVSADWENPYVTLDPQFEADQIRVFGAMAEKGYIYRGA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTDTYIVVWTTTPFTVTAS</entry><entry>240</entry></row><row><entry /><entry /><entry>KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDT+TYIVVWTTTPFTVTAS</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTNTYIVVWTTTPFTVTAS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>RGLTVGPDMEYVVVVPVGSERKYLLAEVLVDSLAAKFGWENFEIVTHHTGKELNHIVTEH</entry><entry>300</entry></row><row><entry /><entry /><entry>RGLTVGPDM+Y+VV P GS+R+Y++AE L+DSLA KFGWE+FE +  H G +L +IVTEH</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>RGLTVGPDMDYLVVKPAGSDRQYVVAEGLLDSLAGKFGWESFETLASHKGADLEYIVTEH</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>PWDTEVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANGLDVVVTVDSRGLMMENA</entry><entry>360</entry></row><row><entry /><entry /><entry>PWDT+VEELVILGDHVT +SGTGIVHTAPGFGEDDYNVG    L+V VTVD RGLMMENA</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>PWDTDVEELVILGDHVTLSSGTGIVHTAPGFGEDDYNVGTKYKLEVAVTVDERGLMMENA</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>GPDFEGQFYDKVTPLVKEKLGDLLLASEVINHSYPFDWRTKKPIIWRAVPQWFASVSKFR</entry><entry>420</entry></row><row><entry /><entry /><entry>GPDF GQFY+KVTP+V +KLGDLLLA EVINHSYPFDWRTKKPIIWRAVPQWFASVS FR</entry><entry /></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GPDFHGQFYNKVTPIVIDKLGDLLLAQEVINHSYPFDWRTKKPIIWRAVPQWFASVSDFR</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>QEILDEIEKTNFQFEWGKKRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT</entry><entry>480</entry></row><row><entry /><entry /><entry>Q+ILDEIEKT F P WG+ RLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT</entry><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>QDILDEIEKTTFHPSWGETRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>DHVADLFAEYGSIVWWQRDARDLLPAGYTHPGSPNGLFEKETDIMDVWFDSGSSWNGVMN</entry><entry>540</entry></row><row><entry /><entry /><entry>DHVADLF E GSI+WWQ++AKDLLP G+THPGSPNG F KETDIMDVWFDSGSSWNGVMN</entry><entry /></row><row><entry>Sbjct:</entry><entry>481</entry><entry>DHVADLFQENGSIIWWQKEAKDLLPEGFTHPGSPNGEFTKETDIMDVWFDSGSSWNGVMN</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>ARENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAVLSQGFVLDGKGEKNSKSL</entry><entry>600</entry></row><row><entry /><entry /><entry> +ENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKA+LSQGFVLDGKGEKMSRS</entry><entry /></row><row><entry>Sbjct:</entry><entry>541</entry><entry>TKENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAILSQGFVLDGKGEKMSKSK</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>GNTILPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILKQTSETYRKIRNTLRFLIANTS</entry><entry>660</entry></row><row><entry /><entry /><entry>GN I P+DV KQ+GA+ILRLWV SVD+ NDVR+SM+IL Q SETYRKIRNTLRFLIANTS</entry><entry /></row><row><entry>Sbjct:</entry><entry>601</entry><entry>GNIISPNDVAKQYGADILRLWVASVDTDNDVRVSMEILGQVSETYRKIRNTLRFLIANTS</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>661</entry><entry>DFNPKQDAVAYENLGAVDRYMTIKFNQVVDTINKAYAAYDFMAIYKAVVNFVTVDLSAFY</entry><entry>720</entry></row><row><entry /><entry /><entry>DFNP  D VAY +LG VD+YMTI FNQ+V TI  AY  YDFMAIYKAVVNFVTVDLSAFY</entry><entry /></row><row><entry>Sbjct:</entry><entry>661</entry><entry>DFNPATDTVAYADLGTVDKYMTIVFNQLVATITDAYERYDFMAIYKAVVNFVTVDLSAFY</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>721</entry><entry>LDFAKDVVYIEAANSPERRRMQTVFYDILVKLTKLLTPILPHTAEEIWSYLEHEEEEFVQ</entry><entry>780</entry></row><row><entry /><entry /><entry>LDFAKDVVYIEAANS ERRRMQTVFYDILVK+TKLLTPILPHT EEIWSYLEHE E FVQ</entry><entry /></row><row><entry>Sbjct:</entry><entry>721</entry><entry>LDFAKDVVYIEAANSLERRRMQTVFYDILVKITKLLTPILPHTTEEIWSYLEHESEAFVQ</entry><entry>780</entry></row><row><entry /></row><row><entry>Query:</entry><entry>781</entry><entry>LAEMPVAQTFSGQEEILEEWSAFMTLRTQAQKALEEARNAKVIGKSLEAHLTIYASQEVK</entry><entry>840</entry></row><row><entry /><entry /><entry>LAEMPVA+TFS QE+ILE WSAFMTLRTQAQKALEEARNAK+IGKSLEAHLTIYAS+EVK</entry><entry /></row><row><entry>Sbjct:</entry><entry>781</entry><entry>LAEMPVAETFSAQEDILEAWSAFMTLRTQAQKALEEARNAKIIGKSLEAHLTIYASEEVK</entry><entry>840</entry></row><row><entry /></row><row><entry>Query:</entry><entry>841</entry><entry>TLLTALNSDIALLMIVSQLTIADEADKPADSVSFEGVAFTVEHAEGEVCERSRRIDPTTK</entry><entry>900</entry></row><row><entry /><entry /><entry>TLLTAL+SDIALL+IVSQLTIAD AD PAD+V+FEGVAF VEHA GEVCERSRRIDPTT+</entry><entry /></row><row><entry>Sbjct:</entry><entry>841</entry><entry>TLLTALDSDIALLLIVSQLTIADLADAPADAVAFEGVAFIVEHAIGEVCERSRRIDPTTR</entry><entry>900</entry></row><row><entry /></row><row><entry>Query:</entry><entry>901</entry><entry>MRSYGVAVCDASAAIIEQYYPEAVAQGFE</entry><entry>929</entry></row><row><entry /><entry /><entry>MRSY   VCD SA IIE+ +PEAVA+GFE</entry><entry /></row><row><entry>Sbjct:</entry><entry>901</entry><entry>MRSYNAFVCDHSAKIIEENFPEAVAEGFE</entry><entry>929</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 75

A DNA sequence (GBSx0075) was identified in <i>S. agalactiae </i>&lt;SEQ ID 247&gt; which encodes the amino acid sequence &lt;SEQ ID 248&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00267" num="00267"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3425(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 249&gt; which encodes the amino acid sequence &lt;SEQ ID 250&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00268" num="00268"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3467(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00269" num="00269"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 77/99 (77%), Positives = 89/99 (89%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MRLINTTSSHPELVRNQLQNTDAKLVEVYSAGNTDVVFTKAPKHYELLISNKYRAIKDEE</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MRLINTTSSHPEL++NQL+NTDA LVEVYSAGNTDV+FT+APKHYELLISNKYRAIK++E</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRLINTTSSHPELIKNQLKNTDAYLVEVYSAGNTDVIFTQAPKHYELLISNKYRAIKEDE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LEAIREFFLKRKIDQSIIIQEQMKSLHTAKLIEISYPTT</entry><entry>99</entry></row><row><entry /><entry /><entry>L+ IREFFLKRKID  I+I  Q K+LHT  LIEIS+ T+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LDIIREFFLKRKIDPRIVIPGQSKTLHTNNLIEISFQTS</entry><entry>99</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 76

A DNA sequence (GBSx0076) was identified in <i>S. agalactiae </i>&lt;SEQ ID 251&gt; which encodes the amino acid sequence &lt;SEQ ID 252&gt;. This protein is predicted to be AP4A hydrolase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00270" num="00270"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 42</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1714(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00271" num="00271"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC06510 GB: AE000676 AP4A hydrolase [<i>Aquifex aeolicus</i>]</entry><entry /></row><row><entry>Identities = 30/101 (29%), Positives = 48/101 (46%),</entry></row><row><entry>Gaps = 2/101 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>32</entry><entry>KIILVQAPNGAWFLPGGEIEENENHLEALTRELIEELGYSATIGHYYGQADEYFYSRHRD</entry><entry>91</entry><entry /></row><row><entry /><entry /><entry>+++L++ P+  W  P G IE  E   E   RE+ EE G    I  Y G+   Y+Y+   +</entry></row><row><entry>Sbjct:</entry><entry>16</entry><entry>EVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEI-HYWYTLKGE</entry><entry>74</entry></row><row><entry /></row><row><entry>Query:</entry><entry>92</entry><entry>TYYYNPAYIYEVTAYHKDQAPLEDFNHLAWFPIQEAKEKLK</entry><entry>132</entry></row><row><entry /><entry /><entry>  +    Y Y +     +  P  +     +FPI+EAK+ LK</entry></row><row><entry>Sbjct:</entry><entry>75</entry><entry>RIFKTVKY-YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLK</entry><entry>114</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 253&gt; which encodes the amino acid sequence &lt;SEQ ID 254&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00272" num="00272"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1954(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00273" num="00273"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 102/149 (68%), Positives = 118/149 (78%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTNPTFGEKIDNVNYRSRFGVYAIIPNPTHDKIILVQAPNGAWFLPGGEIEENENHLEAL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  PTFG K  + +Y +R+GVYAIIPN    KIILVQAPNG+WFLPGGEIE  E  L+AL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MMIPTFGHKNAHKDYVTRYGVYAIIPNHEQTKIILVQAPNGSWFLPGGEIEAGEGQLQAL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TRELIEELGYSATIGHYYGQADEYFYSRHRDTYYYNPAYIYEVTAYHKDQAPLEDFNHLA</entry><entry>120</entry></row><row><entry /><entry /><entry> RELIEELG+SATIG YYGQADEYFYSRHRDT++Y+PAY+YEVTA+     PLEDFN+L</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ERELIEELGFSATIGSYYGQADEYFYSRHRDTHFYHPAYLYEVTAFQAVSKPLEDFNNLG</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>WFPIQEAKEKLKRGSHRWGVQAWEKNHHS</entry><entry>149</entry></row><row><entry /><entry /><entry>WF   EA  KLKR SH+WGV+ W+K HHS</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>WFSPIEAIAKLKRESHQWGVKEWQKKHHS</entry><entry>149</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 77

A DNA sequence (GBSx0077) was identified in <i>S. agalactiae </i>&lt;SEQ ID 255&gt; which encodes the amino acid sequence &lt;SEQ ID 256&gt;. This protein is predicted to be ClpE (clpB-1). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00274" num="00274"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2882(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00275" num="00275"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD01782 GB: AF023421 ClpE [<i>Lactococcus lactis</i>]</entry><entry /></row><row><entry>Identities = 560/752 (74%), Positives = 647/752 (85%), Gaps = 12/752 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLCQNCKLNESTIHLYTNVNGKQKQVDLCQNCYQIIKTDPNNPLFSGLNHVS-HAPGGIN</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>MLCQNC +NE+TIHLYT+VNG++KQ+DLCQNCYQI+K+     LF   N  + ++    N</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLCQNCNINEATIHLYTSVNGQKKQIDLCQNCYQIMKSGGQEALFGAGNASNGNSDEPFN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>PFFDDFFGDLNNFRAFNGQDLPNTPPTQSGGNRGGGNGNGRNNNRNQTATPSQAKGILEE</entry><entry>119</entry></row><row><entry /><entry /><entry>PF +D F  L   + FNG     TPPTQ+GG    G  N R           Q KG+LEE</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PF-NDIFSALQG-QDFNGAASNQTPPTQTGGRGPRGPQNPR---------AKQPKGMLEE</entry><entry>109</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>FGINVTEIARHGDIDPVIGRDSEIIRVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI</entry><entry>179</entry></row><row><entry /><entry /><entry>FGIN+TE AR G+IDPVIGRD EI RVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI</entry></row><row><entry>Sbjct:</entry><entry>110</entry><entry>FGINITESARRGEIDPVIGRDEEIKRVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI</entry><entry>169</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>VDGNVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRQRQDVILFIDEIHEIV</entry><entry>239</entry></row><row><entry /><entry /><entry>VDG+VP KLQ K+VIRLDVVSLVQGTGIRGQFEERMQKLM+EIR+R DVI+FIDEIHEIV</entry></row><row><entry>Sbjct:</entry><entry>170</entry><entry>VDGDVPQKLQNKEVIRLDVVSLVQGTGIRGQFEERMQKLMDEIRKRNDVIMFIDEIHEIV</entry><entry>229</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>GAGTAGEGSMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSVE</entry><entry>299</entry></row><row><entry /><entry /><entry>GAG+AG+G+MDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSV+</entry></row><row><entry>Sbjct:</entry><entry>230</entry><entry>GAGSAGDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSVD</entry><entry>289</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>ETITILKGIQKKYEDYHHVKYNNDAIEAAAVLSNRYIQDRFLPDKAIDLLDEAGSKMNLT</entry><entry>359</entry></row><row><entry /><entry /><entry>ETITIL+GIQ +YEDYHHVKY ++AIEAAA LSNRYIQDRFLPDKAIDLLDE+GSK NLT</entry></row><row><entry>Sbjct:</entry><entry>290</entry><entry>ETITILRGIQARYEDYHHVKYTDEAIEAAAHLSNRYIQDRFLPDKAIDLLDESGSKKNLT</entry><entry>349</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>LNFVDPKEIDQRLIEAENLKAQATREEDYERAAYFRDQIAKYKEMQQQKVDDQDTPIITE</entry><entry>419</entry></row><row><entry /><entry /><entry>L FVDP++I++R+ +AE+ K +AT+ ED+E+AA+FRDQI+K +E+Q+Q+V D+D P+ITE</entry></row><row><entry>Sbjct:</entry><entry>350</entry><entry>LKFVDPEDINRRIADAESKKNEATKAEDFEKAAHFRDQISKLRELQKQEVTDEDMPVITE</entry><entry>409</entry></row><row><entry /></row><row><entry>Query:</entry><entry>420</entry><entry>KTIEHIIEEKTNIPVGDLKEKEQSQLINLADDLKQHVIGQDDAVVKIAKAIRRNRVGLGS</entry><entry>479</entry></row><row><entry /><entry /><entry>K IE I+E+KT IPVGDLKEKEQ+QLINLADDLK HVIGQD+AV KI+KAIRR+RVGLG</entry></row><row><entry>Sbjct:</entry><entry>410</entry><entry>KDIEQIVEQKTQIPVGDLKEKEQTQLINLADDLKAHVIGQDEAVDKISKAIRRSRVGLGK</entry><entry>469</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>PNRPIGSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHAVAKLVGAPPGY</entry><entry>539</entry></row><row><entry /><entry /><entry>PNRPIG FLFVGPTGVGKTEL+KQLA ELFGS++SMIRFDMSEYMEKH+VAKL+GAPPGY</entry></row><row><entry>Sbjct:</entry><entry>470</entry><entry>PNRPIGFFLFVGPTGVGKTELAKQLAKELFGSSESMIRFDMSEYMEKHSVAKLIGAPPGY</entry><entry>529</entry></row><row><entry /></row><row><entry>Query:</entry><entry>540</entry><entry>VGYEEAGQLTEKVRRNPYSLILLDEIEKAHPDVMHMFLQVLDDGRLTDGQGRTVSFKDTI</entry><entry>599</entry></row><row><entry /><entry /><entry>VGYEEAGQLTE+VRRNPYSLILLDEIEKAHPDVMHMFLQ+L+DGRLTD QGRTVSFKD++</entry></row><row><entry>Sbjct:</entry><entry>530</entry><entry>VGYEEAGQLTERVRRNPYSLILLDEIEKAHPDVMHMFLQILEDGRLTDAQGRTVSFKDSL</entry><entry>589</entry></row><row><entry /></row><row><entry>Query:</entry><entry>600</entry><entry>IIMTSNAGSGKTEASVGFGASREGRTNSVLGQLGNFFSPEFMNRFDGIIEFKALDKENLL</entry><entry>659</entry></row><row><entry /><entry /><entry>IIMTSNAG+GK EASVGFGA+REGRT SVLGQLG+FFSPEFMNRFDGIIEF AL KENLL</entry></row><row><entry>Sbjct:</entry><entry>590</entry><entry>IIMTSNAGTGKVEASVGFGAAREGRTKSVLGQLGDFFSPEFMNRFDGIIEFSALSKENLL</entry><entry>649</entry></row><row><entry /></row><row><entry>Query:</entry><entry>660</entry><entry>NIVDIMLSDVNARLAINGIHLDVTDKVKEKLVDLGYDPKMGARPLRRTIQEHIEDAITDY</entry><entry>719</entry></row><row><entry /><entry /><entry> IVD+ML +VN ++  N IHL VT   KEKLVDLGY+P MGARPLRR IQE+IED+I D+</entry></row><row><entry>Sbjct:</entry><entry>650</entry><entry>KIVDLMLDEVNEQIGRNDIHLSVTQAAKEKLVDLGYNPAMGARPLRRIIQENIEDSIADF</entry><entry>709</entry></row><row><entry /></row><row><entry>Query:</entry><entry>720</entry><entry>YLENPSEKELRAIMTSNGNIIIKSSKKTEEST</entry><entry>751</entry></row><row><entry /><entry /><entry>Y+E+P  K+L A +  +  +I   +++T E+T</entry></row><row><entry>Sbjct:</entry><entry>710</entry><entry>YIEHPEYKQLVADLIDDKIVISNQTQETAETT</entry><entry>741</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 257&gt; which encodes the amino acid sequence &lt;SEQ ID 258&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00276" num="00276"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3104(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00277" num="00277"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 640/751 (85%), Positives = 691/751 (91%), Gaps = 7/751 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLCQNCKLNESTIHLYTNVNGKQKQVDLCQNCYQIIKTDPNNPLFSGLNHVSHAPG-GIN</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>MLCQNC LNESTIHLYT+VNGKQ+QVDLCQNCYQI+K+DP N + +GL     A     +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLCQNCNLNESTIHLYTSVNGKQRQVDLCQNCYQIMKSDPANSILNGLTPGYRAQDRSTS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>PFFDDFFGDLNNFRAFNGQDLPNTPPTQSGGNRGGGNGNGRNNNRNQTATPS----QAKG</entry><entry>115</entry></row><row><entry /><entry /><entry>PFFDDFFGDLNNFRAF   +LPNTPPTQ+G N  GG   G N N  + A P     QAKG</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PFFDDFFGDLNNFRAFG--NLPNTPPTQAGQNGNGGGRYGGNYNGQRPAQPQTPNQQAKG</entry><entry>118</entry></row><row><entry /></row><row><entry>Query:</entry><entry>116</entry><entry>ILEEFGINVTEIARHGDIDPVIGRDSEIIRVIEILNRRTKNNPVLIGEPGVGKTAVVEGL</entry><entry>175</entry></row><row><entry /><entry /><entry>+LEEFGINVT+IAR+G+IDPVIGRD EI RVIEILNRRTKNNPVLIGEPGVGKTAVVEGL</entry></row><row><entry>Sbjct:</entry><entry>119</entry><entry>LLEEFGINVTDIARNGNIDPVIGRDEEITRVIEILNRRTKNNPVLIGEPGVGKTAVVEGL</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>AQKIVDGNVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRQRQDVILFIDEI</entry><entry>235</entry></row><row><entry /><entry /><entry>AQKI+DG VP KLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIR R+DVILFIDEI</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>AQKIIDGTVPQKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRNRKDVILFIDEI</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>HEIVGAGTAGEGSMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE</entry><entry>295</entry></row><row><entry /><entry /><entry>HEIVGAG+AG+G+MDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>HEIVGAGSAGDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>PSVEETITILKGIQKKYEDYHHVKYNNDAIEAAAVLSNRYIQDRFLPDKAIDLLDEAGSK</entry><entry>355</entry></row><row><entry /><entry /><entry>PSVEETITILKGIQ KYEDYHHVKY+  AIEAAA LSNRYIQDRFLPDKAIDLLDEAGSK</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>PSVEETITILKGIQPKYEDYHHVKYSPAAIEAAAHLSNRYIQDRFLPDKAIDLLDEAGSK</entry><entry>358</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>MNLTLNFVDPKEIDQRLIEAENLKAQATREEDYERAAYFRDQIAKYKEMQQQKVDDQDTP</entry><entry>415</entry></row><row><entry /><entry /><entry>MNLTLNFVDPKEID+RLIEAENLKAQATR+EDYERAAYFRDQI KYKEMQ QKVD+QD P</entry></row><row><entry>Sbjct:</entry><entry>359</entry><entry>MNLTLNFVDPKEIDKRLIEAENLKAQATRDEDYERAAYFRDQITKYKEMQAQKVDEQDIP</entry><entry>418</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>IITEKTIEHIIEEKTNIPVGDLKEKEQSQLINLADDLKQHVIGQDDAVVKIAKAIRRNRV</entry><entry>475</entry></row><row><entry /><entry /><entry>IITEKTIE I+E+KTNIPVGDLKEKEQSQL+NLA+DLK HVIGQDDAV KIAKAIRRNRV</entry></row><row><entry>Sbjct:</entry><entry>419</entry><entry>IITEKTIEAIVEQKTNIPVGDLKEKEQSQLVNLANDLKAHVIGQDDAVDKIAKAIRRNRV</entry><entry>478</entry></row><row><entry /></row><row><entry>Query:</entry><entry>476</entry><entry>GLGSPNRPIGSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHAVAKLVGA</entry><entry>535</entry></row><row><entry /><entry /><entry>GLG+PNRPIGSFLFVGPTGVGKTELSKQLAIELFGS ++MIRFDMSEYMEKHAVAKLVGA</entry></row><row><entry>Sbjct:</entry><entry>479</entry><entry>GLGTPNRPIGSFLFVGPTGVGKTELSKQLAIELFGSTNNMIRFDMSEYMEKHAVAKLVGA</entry><entry>538</entry></row><row><entry /></row><row><entry>Query:</entry><entry>536</entry><entry>PPGYVGYEEAGQLTEKVRRNPYSLILLDEIEKAHPDVMHMFLQVLDDGRLTDGQGRTVSF</entry><entry>595</entry></row><row><entry /><entry /><entry>PPGY+GYEEAGQLTE+VRRNPYSLILLDE+EKAHPDVMHMFLQVLDDGRLTDGQGRTVSF</entry></row><row><entry>Sbjct:</entry><entry>539</entry><entry>PPGYIGYEEAGQLTEQVRRNPYSLILLDEVEKAHPDVMHMFLQVLDDGRLTDGQGRTVSF</entry><entry>598</entry></row><row><entry /></row><row><entry>Query:</entry><entry>596</entry><entry>KDTIIIMTSNAGSGKTEASVGFGASREGRTNSVLGQLGNFFSPEFMNRFDGIIEFKALDK</entry><entry>655</entry></row><row><entry /><entry /><entry>KDTIIIMTSNAG+GK+EASVGFGA+REGRT+SVLG+L NFFSPEFMNRFDGIIEFKAL K</entry></row><row><entry>Sbjct:</entry><entry>599</entry><entry>KDTIIIMTSNAGTGKSEASVGFGAAREGRTSSVLGELSNFFSPEFMNRFDGIIEFKALSK</entry><entry>658</entry></row><row><entry /></row><row><entry>Query:</entry><entry>656</entry><entry>ENLLNIVDIMLSDVNARLAINGIHLDVTDKVKEKLVDLGYDPKMGARPLRRTIQEHIEDA</entry><entry>715</entry></row><row><entry /><entry /><entry>E+LL+IVD+ML DVN RL  NGIHLDVT KVKEKLVDLGYDPKMGARPLRRTIQ++IEDA</entry></row><row><entry>Sbjct:</entry><entry>659</entry><entry>EHLLHIVDLMLEDVNERLGYNGIHLDVTQKVKEKLVDLGYDPKMGARPLRRTIQDYIEDA</entry><entry>718</entry></row><row><entry /></row><row><entry>Query:</entry><entry>716</entry><entry>ITDYYLENPSEKELRAIMTSNGNIIIKSSKK</entry><entry>746</entry></row><row><entry /><entry /><entry>ITDYYLE+P+EK+LRA+MT++ NI IK+ K+</entry></row><row><entry>Sbjct:</entry><entry>719</entry><entry>ITDYYLEHPTEKQLRALMTNSENITIKAVKE</entry><entry>749</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 78

A DNA sequence (GBSx0078) was identified in <i>S. agalactiae </i>&lt;SEQ ID 259&gt; which encodes the amino acid sequence &lt;SEQ ID 260&gt;. This protein is predicted to be glutamine ABC transporter, permease protein (glnP). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00278" num="00278"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="98pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.92</entry><entry>Transmembrane</entry><entry>  27-43 (15-46)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.50</entry><entry>Transmembrane</entry><entry>200-216 (196-217)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4970(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9619&gt; which encodes amino acid sequence &lt;SEQ ID 9620&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00279" num="00279"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB91000 GB: AE001090 glutamine ABC transporter, permease protein</entry><entry /></row><row><entry>(glnP) [<i>Archaeoglobus fulgidus</i>]</entry></row><row><entry>Identities = 92/209 (44%), Positives = 129/209 (61%), Gaps = 10/209 (4%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>17</entry><entry>YGVMVTIMISTCVVFFGTIIGVLIALVKRTNLHFLTILANFYVWVFRGTPMVVQIMIAFA</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>+G  VT+ ++   +FFG IIG +  L + +       ++  YV V RGTP++VQI+I +</entry><entry /></row><row><entry>Sbjct:</entry><entry>21</entry><entry>FGASVTLKLTLISIFFGLIIGTIAGLGRVSKNPLPFAISTAYVEVIRGTPLLVQILIVYF</entry><entry>80</entry></row><row><entry /></row><row><entry>Query:</entry><entry>77</entry><entry>WMHFNNLPTISFGVLDLDFTRLLPGIIIISLNSGAYISEIVRAGIEAVPSGQIEAAYSLG</entry><entry>136</entry></row><row><entry /><entry /><entry>      LP I   +          GII +S+ SGAYI+EIVRAGIE++P GQ+EAA SLG</entry><entry /></row><row><entry>Sbjct:</entry><entry>81</entry><entry>-----GLPAIGINLQPEP-----AGIIALSICSGAYIAEIVRAGIESIPIGQMEAARSLG</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>137</entry><entry>IRPKNTLRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELWNGAQSVVTATYSPV</entry><entry>196</entry></row><row><entry /><entry /><entry>+     +RYVI PQAF+NILPALGNEFI ++KDS+LL  I ++EL    + +V  T++</entry><entry /></row><row><entry>Sbjct:</entry><entry>131</entry><entry>MTYLQAMRYVIFPQAFRNILPALGNEFIALLKDSSLLSVISIVELTRVGRQIVNTTFNAW</entry><entry>190</entry></row><row><entry /></row><row><entry>Query:</entry><entry>197</entry><entry>APLLFAAFYYLMLTTILSALLKQMEKYLG</entry><entry>225</entry></row><row><entry /><entry /><entry> P L  A +YLM+T  LS L+   +K LG</entry><entry /></row><row><entry>Sbjct:</entry><entry>191</entry><entry>TPFLGVALFYLMMTIPLSRLVAYSQKKLG</entry><entry>219</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 261&gt; which encodes the amino acid sequence &lt;SEQ ID 262&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00280" num="00280"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="98pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.08</entry><entry>Transmembrane</entry><entry>  25-41 (11-44)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.91</entry><entry>Transmembrane</entry><entry>202-218 (201-218)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4630(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00281" num="00281"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB91000 GB: AE001090 glutamine ABC transporter, permease protein</entry><entry /></row><row><entry>(glnP) [<i>Archaeoglobus fulgidus</i>]</entry></row><row><entry>Identities = 91/209 (43%), Positives = 138/209 (65%), Gaps = 12/209 (5%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>15</entry><entry>YGVLVTIMISVSVVFFGTLIGVLVTLIKRSHVKPLTWVVNL-YVWIFRGTPMVVQIMIAF</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>+G  VT+ +++  +FFG +IG +  L + S   PL + ++  YV + RGTP++VQI+I +</entry><entry /></row><row><entry>Sbjct:</entry><entry>21</entry><entry>FGASVTLKLTLISIFFGLIIGTIAGLGRVSK-NPLPFAISTAYVEVIRGTPLLVQILIVY</entry><entry>79</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>AWMHFNNMPTIGFGVLDLDFSRLLPGIIIISLNSGAYISEIVRAGIEAVPKGQLEAAYSL</entry><entry>133</entry></row><row><entry /><entry /><entry>       +P IG     ++      GII +S+ SGAYI+EIVRAGIE++P GQ+EAA SL</entry><entry /></row><row><entry>Sbjct:</entry><entry>80</entry><entry>F-----GLPAIG-----INLQPEPAGIIALSICSGAYIAEIVRAGIESIPIGQMEAARSL</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>134</entry><entry>GIRPQNAMRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELWNGAQSVVTATYSP</entry><entry>193</entry></row><row><entry /><entry /><entry>G+    AMRYVI PQAF+NILPALGNEFI ++KDS+LL  I ++EL    + +V  T++</entry><entry /></row><row><entry>Sbjct:</entry><entry>130</entry><entry>GMTYLQAMRYVIFPQAFRNILPALGNEFIALLKDSSLLSVISIVELTRVGRQIVNTTFNA</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>194</entry><entry>ISPLLVAAFYYLMVTTVMAQLLAVLERHM</entry><entry>222</entry></row><row><entry /><entry /><entry> +P L  A +YLM+T  +++L+A  ++ +</entry><entry /></row><row><entry>Sbjct:</entry><entry>190</entry><entry>WTPFLGVALFYLMMTIPLSRLVAYSQKKL</entry><entry>218</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00282" num="00282"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 180/225 (80%), Positives = 208/225 (92%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MNFSFLPQYWSYFNYGVMVTIMISTCVVFFGTIIGVLIALVKRTNLHFLTILANFYVWVF</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>M+ SFLP+YW+YFNYGV+VTIMIS  VVFFGT+IGVL+ L+KR+++  LT + N YVW+F</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MDLSFLPKYWAYFNYGVLVTIMISVSVVFFGTLIGVLVTLIKRSHVKPLTWVVNLYVWIF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>RGTPMVVQIMIAFAWMHFNNLPTISFGVLDLDFTRLLPGIIIISLNSGAYISEIVRAGIE</entry><entry>122</entry></row><row><entry /><entry /><entry>RGTPMVVQIMIAFAWMHFNN+PTI FGVLDLDF+RLLPGIIIISLNSGAYISEIVRAGIE</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>RGTPMVVQIMIAFAWMHFNNMPTIGFGVLDLDFSRLLPGIIIISLNSGAYISEIVRAGIE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>AVPSGQIEAAYSLGIRPKNTLRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW</entry><entry>182</entry></row><row><entry /><entry /><entry>AVP GQ+EAAYSLGIRP+N +RYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>AVPKGQLEAAYSLGIRPQNAMRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>NGAQSVVTATYSPVAPLLFAAFYYLMLTTILSALLKQMEKYLGKG</entry><entry>227</entry></row><row><entry /><entry /><entry>NGAQSVVTATYSP++PLL AAFYYLM+TT+++ LL  +E+++ +G</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>NGAQSVVTATYSPISPLLVAAFYYLMVTTVMAQLLAVLERHMAQG</entry><entry>225</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 79

A DNA sequence (GBSx0079) was identified in <i>S. agalactiae </i>&lt;SEQ ID 263&gt; which encodes the amino acid sequence &lt;SEQ ID 264&gt;. This protein is predicted to be phosphomannomutase (manB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00283" num="00283"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 60</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5400(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9621&gt; which encodes amino acid sequence &lt;SEQ ID 9622&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00284" num="00284"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB04825 GB: AP001510 phosphomannomutase [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 239/548 (43%), Positives = 344/548 (62%), Gaps = 14/548 (2%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>MNYKEIYQEWLENDSLGKDIKSDLEAIKGDESEIQDRFYKTLEFGTAGLRGKLGAGTNRN</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>M++++ Y++W   + L  ++K  LEAI GD +++D FYK LEFGT G+RG++G G NRN</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSWRQRYEKWKGFNELELELKQSLEAIGGDEQQLEDCFYKNLEFGTGGMRGEIGPGPNRM</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>NTYMVGKAAQALANTIIDHGPEAIARGIAVSYDVRYQSKEFAELTCSIMAANGIKSYIYK</entry><entry>123</entry></row><row><entry /><entry /><entry>NTY + KA++  A  +++ G    A+G+ ++YD  R++S EFA      +  +GIK+Y+++</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>NTYTIRKASEGFARYLLEQGEHVKAQGVVIAYDSRHKSPEFAREAALTIGKHGIKAYLFE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>GIRPTPMCSYAIRALGCVSGVMITASHNPQAYNGYKAYWKEGSQILDDIADQIANHMDAI</entry><entry>183</entry></row><row><entry /><entry /><entry> +RPTP  S+A+R LG   G++ITASHNP  YNG+K Y  +G Q+  + A+++   ++ I</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>ELRPTPELSFAVRKLGAAGGIVITASHNPPEYNGFKVYGSDGCQLPPEPANRLVKFVNEI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>184</entry><entry>TDYQQIKQIPFEEALASGSASYIDESIEEAYKKEVLGLTINDTNID---KSVRVVYTPLN</entry><entry>240</entry></row><row><entry /><entry /><entry> D   I      E   +G+   I E ++ AY + +  + +N   ++   K VR+V+TPL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>EDELVIPVGDERELKENGTLEMIGEEVDVAYHEALKTIIVNPELLEASAKDVRIVFTPLH</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKAFAYSESLGKSVDADI</entry><entry>300</entry></row><row><entry /><entry /><entry>G  NLPVR VL   GFENV VV EQE+PDP F+TV  PNPE   AFA +   GK  +AD+</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GTANLPVRRVLEAVGFENVTVVKEQELPDPQFSTVKAPNPEEHAAFALAIEYGKKTEADV</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>LLATDPDCDRVALEVKDSKGEYIFLNGNKIGALLSYYIFSQRCALGNLPHHPVLVKSIVT</entry><entry>360</entry></row><row><entry /><entry /><entry>L+ATDPD DRV + V++  GEYI L GN+ G L+ +Y+ SQ+   G LP + + +K+IVT</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LIATDPDADRVGVAVQNQAGEYIVLTGNQTGGLMLHYLLSQKKEKGQLPVNGIALKTIVT</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>GDLSKVIADKYNIETVETLTGFKNICGKANEYDISKDKTYLFGYEESIGFCYGTFVRDKD</entry><entry>420</entry></row><row><entry /><entry /><entry> +  + IA+ + I  V+TLTGFK I  K  EY + S +  +LFGYEES G+  G FVRDKD</entry><entry /></row><row><entry>Sbjct:</entry><entry>361</entry><entry>SEFGRAIAEDFGIPMVDTLTGFKFIGEKIKEYEQSGEHQFLFGYEESYGYLIGDFVRDKD</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>AVSASMMVVEMTAYYKERGQTLLDVLQTIYDKFGYYNERQFSLELEGAEGQERISRIMED</entry><entry>480</entry></row><row><entry /><entry /><entry>AV A ++  EMTAYYK RG TL D L  ++D++GYY E   S+ L+G  G E+I  ++</entry><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>AVQACLLAAEMTAYYKSRGMTLYDGLLELFDRYGYYREGLTSITLKGKVGVEKIQHVLSQ</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>FRQDPILQVGEMTLENSIDFKDGYK-----------DFPKQNCLKYYFNEGSWYALRPSG</entry><entry>529</entry></row><row><entry /><entry /><entry>FRQ P  QV +  +    D++   K             P  N LKY   +GSW+ LRPSG</entry><entry /></row><row><entry>Sbjct:</entry><entry>481</entry><entry>FRQSPPKQVNDQQVVVIEDYQTKEKVSVKERTVEAITLPTSNVLKYMLEDGSWFCLRPSG</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>530</entry><entry>TEPKIKCY</entry><entry>537</entry></row><row><entry /><entry /><entry>TEPK+K Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>541</entry><entry>TEPKLKIY</entry><entry>548</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 265&gt; which encodes the amino acid sequence &lt;SEQ ID 266&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00285" num="00285"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5487(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00286" num="00286"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 470/564 (83%), Positives = 517/564 (91%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSHMNYKEIYQEWLENDSLGKDIKSDLEAIKGDESEIQDRFYKTLEFGTAGLRGKLGAGT</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MS+M Y E+YQEWL N+ L  DIK+DL AIK +E+EIQDRFYKTLEFGTAGLRGKLGAGT</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSNMTYNEVYQEWLHNNDLSDDIKADLAAIKDNEAEIQDRFYKTLEFGTAGLRGKLGAGT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NRMNTYMVGKAAQALANTIIDHGPEAIARGIAVSYDVRYQSKEFAELTCSIMAANGIKSY</entry><entry>120</entry></row><row><entry /><entry /><entry>NRMNTYMVGKAAQALANTIIDHGPEA+ +GIAVSYDVRYQS+ FAELTCSIMAANGIK+Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>NRMNTYMVGKAAQALANTIIDHGPEAVKKGIAVSYDVRYQSRTFAELTCSIMAANGIKAY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IYKGIRPTPMCSYAIRALGCVSGVMITASHNPQAYNGYKAYWKEGSQILDDIADQIANHM</entry><entry>180</entry></row><row><entry /><entry /><entry>+YKGIRPTPMCSYAIRALGC+SGVMITASHNPQAYNGYKAYW+EGSQILDDIADQIA HM</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LYKGIRPTPMCSYAIRALGCISGVMITASHNPQAYNGYKAYWQEGSQILDDIADQIAQHM</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>DAITDYQQIKQIPFEEALASGSASYIDESIEEAYKKEVLGLTINDTNIDKSVRVVYTPLN</entry><entry>240</entry></row><row><entry /><entry /><entry> A+T YQ+IKQ+PFE+AL SG  +YIDESIEEAYKKEVLGLTINDT+IDKSVRVVYTPLN</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>AALTQYQEIKQMPFEKALDSGLVTYIDESIEEAYKKEVLGLTINDTDIDKSVRVVYTPLN</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKAFAYSESLGKSVDADI</entry><entry>300</entry></row><row><entry /><entry /><entry>GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPK FAYSE LGK+VDADI</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKTFAYSEKLGKAVDADI</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>LLATDPDCDRVALEVKDSKGEYIFLNGNKIGALLSYYIFSQRCALGNLPHHPVLVKSIVT</entry><entry>360</entry></row><row><entry /><entry /><entry>L+ATDPDCDRVALEVK++ G+Y+FLNGNKIGALLSYYIFSQR  LGNLP +PVLVKSIVT</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LIATDPDCDRVALEVKNAVGDYVFLNGNKIGALLSYYIFSQRFDLGNLPANPVLVKSIVT</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>GDLSKVIADKYNIETVETLTGFKNICGKANEYDISKDKTYLFGYEESIGFCYGTFVRDKD</entry><entry>420</entry></row><row><entry /><entry /><entry>GDLS+ IA  Y IETVETLTGFKNICGKANEYD++K K YLFGYEESIGFCYGTFVRDKD</entry><entry /></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GDLSRAIASHYGIETVETLTGFKNICGKANEYDVTKQKNYLFGYEESIGFCYGTFVRDKD</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>AVSASMMVVEMTAYYKERGQTLLDVLQTIYDKFGYYNERQFSLELEGAEGQERISRIMED</entry><entry>480</entry></row><row><entry /><entry /><entry>AVSASMM+VEM AYYK++GQ LLDVLQTIY  FGYYNERQ +LELEG EGQ+RI+RIMED</entry><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>AVSASMMIVEMAAYYKKKGQNLLDVLQTIYATFGYYNERQIALELEGIEGQKRIARIMED</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>FRQDPILQVGEMTLENSIDFKDGYKDFPKQNCLKYYFNEGSWYALRPSGTEPKIKCYLYT</entry><entry>540</entry></row><row><entry /><entry /><entry>FRQ PI  V EM L+ +IDF DGY+DFPKQNCLK+Y ++GSWYALRPSGTEPKIK YLYT</entry><entry /></row><row><entry>Sbjct:</entry><entry>481</entry><entry>FRQTPIASVAEMALDKTIDFIDGYQDFPKQNCLKFYLDDGSWYALRPSGTEPKIKFYLYT</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>IGCTEADSLSKLNAIESACRAKMN</entry><entry>564</entry></row><row><entry /><entry /><entry>IG T+ +S +KL+AIE+ACR K+N</entry><entry /></row><row><entry>Sbjct:</entry><entry>541</entry><entry>IGQTQENSATKLDAIEAACRTKIN</entry><entry>564</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 80

A DNA sequence (GBSx0080) was identified in <i>S. agalactiae </i>&lt;SEQ ID 267&gt; which encodes the amino acid sequence &lt;SEQ ID 268&gt;. This protein is predicted to be methylenetetrahydrofolate dehydrogenase (folD). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00287" num="00287"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4672(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00288" num="00288"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC44612 GB: U58210 tetrahydrofolate dehydrogenase/cyclohydrolase</entry><entry /></row><row><entry>[<i>Streptococcus thermophilus</i>]</entry></row><row><entry>Identities = 209/282 (74%), Positives = 248/282 (87%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTELIDGKALSQKMQAELGRKVERLKEQHGIIPGLAVILVGDNPASQVYVRNKERSALEA</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  ++DGKAL+  MQ +L  KV RLKE+  I+PGL VI+VG+NPASQVYVRNKER+A +A</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAIIMDGKALAVNMQEQLQEKVARLKEKEWIVPGLVVIMVGENPASQVYVRNKERAAKKA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GFKSETLRLSESISQEELIDIIHQYNEDKSIHGILVQLPLPQHINDKKIILAIDPKKDVD</entry><entry>120</entry></row><row><entry /><entry /><entry>GF S+T+ LSESIS+EELI++I +YN++   HGILVQLPLP HIN+ +I+LAIDPKKDVD</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GFHSKTVNLSESISEEELIEVIEKYNQNPLFHGILVQLPLPNHINEMRILLAIDPKKDVD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GFHPMNTGHLWSGRPMMVPCTPAGIMEMFREYHVDLEGKHAVIIGRSNIVGKPMAQLLLD</entry><entry>180</entry></row><row><entry /><entry /><entry>GFHPMNTG+LW+GRP MVPCTPAGIME+ REY+V+LEGK AVIIGRSNIVGKPMAQLLL+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GFHPMNTGNLWNGRPQMVPCTPAGIMEILREYNVELEGKTAVIIGRSNIVGKPMAQLLLE</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KNATVTLTHSRTRNLSEVTKEADILIVAIGQGHFVTKDFVKEGAVVIDVGMNRDENGKLI</entry><entry>240</entry></row><row><entry /><entry /><entry>KNATVTLTHSRT +L++V  +AD+LIVAIG+  FVT++FVKEGAVVIDVG+NRDE GKL</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KNATVTLTHSRTPHLAKVCNKADVLIVAIGRAKFVTEEFVKEGAVVIDVGINRDEEGKLC</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDVVFEQVAEVASMITPVPGGVGPMTITMLLEQTYQAALRSV</entry><entry>282</entry></row><row><entry /><entry /><entry>GDV F+QV E  SMITPVPGGVGPMTITML+EQTYQAALRS+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GDVDFDQVKEKVSMITPVPGGVGPMTITMLMEQTYQAALRSL</entry><entry>282</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 269&gt; which encodes the amino acid sequence &lt;SEQ ID 270&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00289" num="00289"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3368(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00290" num="00290"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 230/281 (81%), Positives = 257/281 (90%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTELIDGKALSQKMQAELGRKVERLKEQHGIIPGLAVILVGDNPASQVYVRNKERSALEA</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTELIDGKAL+QKMQ EL  KV  LK++ GI+PGLAVILVGD+PASQVYVRNKER+AL</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>MTELIDGKALAQKMQQELAAKVNNLKQKKGIVPGLAVILVGDDPASQVYVRNKERAALTV</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GFKSETLRLSESISQEELIDIIHQYNEDKSIHGILVQLPLPQHINDKKIILAIDPKKDVD</entry><entry>120</entry></row><row><entry /><entry /><entry>GFKSET+RLSE I QEELI +I +YN D +IHGILVQLPLP HINDKKIILAIDPKKDVD</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>GFKSETVRLSEFICQEELIAVIERYNADNTIHGILVQLPLPNHINDKKIILAIDPKKDVD</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GFHPMNTGHLWSGRPMMVPCTPAGIMEMFREYHVDLEGKHAVIIGRSNIVGKPMAQLLLD</entry><entry>180</entry></row><row><entry /><entry /><entry>GFHPMNTGHLWSGRP+MVPCTP+GIME+ REY+V+LEGKHAVIIGRSNIVGKPMAQLLLD</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>GFHPMNTGHLWSGRPLMVPCTPSGIMELLREYNVNLEGKHAVIIGRSNIVGKPMAQLLLD</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KNATVTLTHSRTRNLSEVTKEADILIVAIGQGHFVTKDFVKEGAVVIDVGMNRDENGKLI</entry><entry>240</entry></row><row><entry /><entry /><entry>KNATVTLTHSRTR L EV + AD+LIVAIGQGHF+TK ++K+GA+VIDVGMNRD+NGKLI</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>KNATVTLTHSRTRQLEEVCRCADVLIVAIGQGHFITKQYIKDGAIVIDVGMNRDDNGKLI</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDVVFEQVAEVASMITPVPGGVGPMTITMLLEQTYQAALRS</entry><entry>281</entry></row><row><entry /><entry /><entry>GDV F++VAEVA+ ITPVPGGVGPMTI MLLEQTYQ+ALRS</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>GDVAFDEVAEVAAKITPVPGGVGPMTIAMLLEQTYQSALRS</entry><entry>283</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 81

A DNA sequence (GBSx0081) was identified in <i>S. agalactiae </i>&lt;SEQ ID 271&gt; which encodes the amino acid sequence &lt;SEQ ID 272&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00291" num="00291"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="189pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.24</entry><entry>Transmembrane</entry><entry>39-55 (38-58)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2296(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9623&gt; which encodes amino acid sequence &lt;SEQ ID 9624&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00292" num="00292"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC44613 GB:U58210 orf1091 [<i>Streptococcus thermophilus</i>]</entry><entry /></row><row><entry>Identities = 149/277 (53%), Positives = 191/277 (68%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MIVGEQEARALIKPRPKSSHKGDYGSVLLIGGFYPYGGAIIMAALACVKTGAGLVTVATQ</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M V +   R +I+PR + SHKG YG VLL+GG YPYGGAIIMAA+ACV +GAGLVTVAT</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKVDDDLVRQVIRPRLRGSHKGSYGRVLLVGGLYPYGGAIIMAAIACVNSGAGLVTVATD</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>SCNIPSLHSQLPEVMAFDSDDYKWLEKSIVQSDVIVIGPGLGVSESSRKILNQTMEKIQS</entry><entry>120</entry></row><row><entry /><entry /><entry>  NI +LH+ LPE MAFD  + +     +  +DVI+IG GLG  E++   L   +  I+S</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>RENIIALHAHLPEAMAFDLRETERFLDKLRAADVILIGSGLGEEETADWALELVLANIRS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HQSVILDGSALTLLSEGAFPQTKAKNLVLTPHQKEWERLSGIAVSQQTKENTQTALKSFP</entry><entry>180</entry></row><row><entry /><entry /><entry>+Q++++DGSAL LL++         +L+LTPHQKEWERLSG+A+S+Q+  NTQ AL+ F</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NQNLVVDGSALNLLAKKNQSSLPKCHLILTPHQKEWERLSGLAISEQSVSNTQRALEEFQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>KGTILVAKSSHTRIFQDLDEKEIIVGGPYQATGGMGDTLCGMIAGMLAQFKEASPLDKVS</entry><entry>240</entry></row><row><entry /><entry /><entry> GTILVAKS  T ++Q  +   + VGGPYQATGGMGDTL GM+AG LAQF        V</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SGTILVAKSHKTAVYQGAEVTHLEVGGPYQATGGMGDTLAGMVAGFLAQFASTDSYKAVI</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VGVYLHSAIAQGLSKEAYVVLPTTISDEIPKEMARLS</entry><entry>277</entry></row><row><entry /><entry /><entry>V  +LHSAIA  +++ AYVVLPT IS  IP  M +LS</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>VATWLHSAIADNIAENAYVVLPTRISKAIPSWMKKLS</entry><entry>277</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

SEQ ID 272 (GBS413) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 79</figref> (lane 2; MW 34.2 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 171</figref> (lane 7; MW 59 kDa).

GBS413-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 218</figref>, lane 12.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 82

A DNA sequence (GBSx0082) was identified in <i>S. agalactiae </i>&lt;SEQ ID 273&gt; which encodes the amino acid sequence &lt;SEQ ID 274&gt;. This protein is predicted to be Exonuclease VII large subunit (xseA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00293" num="00293"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3172(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00294" num="00294"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB14361 GB:Z99116 similar to exodeoxyribonuclease VII (large</entry><entry /></row><row><entry>subunit) [<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 193/446 (43%), Positives = 283/446 (63%), Gaps = 10/446 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>YLSVSTLTKYLKLKFDKDPYLERVYLTGQVSNFR-RRPNHQYFSLKDDKSVIQATMWSGH</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>Y++VS LTKY+K KFD DP+LE +++ G++SN +     H YF+LK+ K  +Q+ M++</entry><entry /></row><row><entry>Sbjct:</entry><entry>6</entry><entry>YVTVSALTKYIKRKFDVDPHLENIWIKGELSNVKIHTRGHIYFTLKERKGRMQSVMFARQ</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>FKKLGFELEEGMKVNVVGRVQLYEPSGSYSIIVEKAEPDGIGALAIQFEQLKKKLSQAGY</entry><entry>122</entry></row><row><entry /><entry /><entry> ++L F+ E GMKV V G + +YEPSG+Y +  ++ +PDG+GAL + +E+LKKKL+  G</entry><entry /></row><row><entry>Sbjct:</entry><entry>66</entry><entry>SERLPFKPENGMKVLVRGGISVYEPSGNYQLYAKEMQPDGVGALYLAYEELKKKLAGEGL</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>FDDRHKQLIPQFVRKIGVVTSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGEGAAQEIA</entry><entry>182</entry></row><row><entry /><entry /><entry>FDDR+K+ IP F   IGVVTSP+GA +RD+ITT+ RR+P V++++ P  VQGE A++ I</entry><entry /></row><row><entry>Sbjct:</entry><entry>126</entry><entry>FDDRYKKQIPAFPATIGVVTSPTGAAVRDVITTLKRRYPLVKVIVLPALVQGENASRSIV</entry><entry>185</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>QTIALANEKKDLDLLIVGRGGGSIEDLWAFNEECVVEAIFESRLPVISSVGHETDTTLAD</entry><entry>242</entry></row><row><entry /><entry /><entry>  I  ANEK+  D+LIVGRGGGSIE+LWAFNEE V  AIF S +P+IS+VGHETD T++D</entry><entry /></row><row><entry>Sbjct:</entry><entry>186</entry><entry>TRIEEANEKEICDVLIVGRGGGSIEELWAFNEEIVARAIFASNIPIISAVGHETDFTISD</entry><entry>245</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>FVADRRAATPTAAAELATPVTKIDILSWITERENRMYQSSLRLIRTKEERLQKSKQSVIF</entry><entry>302</entry></row><row><entry /><entry /><entry>FVAD RAATPT AAE+A P T  D++      E RM ++  + +  ++ R+Q  + S  F</entry><entry /></row><row><entry>Sbjct:</entry><entry>246</entry><entry>FVADIRAATPTGAAEIAVPHT-TDLIERTKTAEVRMTRAMQQHLGQEKGRIQTLQSSYAF</entry><entry>304</entry></row><row><entry /></row><row><entry>Query:</entry><entry>303</entry><entry>RQPERLYDGFLQKLD----NLNQQLTYSMRDKLQTVRQKQGLLHQKLQGIDLKQRIHIYQ</entry><entry>358</entry></row><row><entry /><entry /><entry>R P+RLY    Q+ D        QLT  +  K + + ++   L        LKQ    YQ</entry><entry /></row><row><entry>Sbjct:</entry><entry>305</entry><entry>RFPKRLYAQKEQQFDLAYQQFQAQLTALLDRKSRQLERETYRLEALHPHEQLKQARTRYQ</entry><entry>364</entry></row><row><entry /></row><row><entry>Query:</entry><entry>359</entry><entry>ERVVQSRRLLSSTMTSQYDSKLARFEKAQDALISLDSSRIVARGYAIIEKNHTLVSTTNG</entry><entry>418</entry></row><row><entry /><entry /><entry>E+  Q R+     M  Q     ++F+     L +L   +++ RGY++  K   L+ + +</entry><entry /></row><row><entry>Sbjct:</entry><entry>365</entry><entry>EQTNQLRK----NMNIQMKQLHSQFQTVLGKLNALSPLQVMERGYSLAYKEDKLIKSVSQ</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>419</entry><entry>INEGDHLQVKMQDGLLEVEVKDVRQE</entry><entry>444</entry></row><row><entry /><entry /><entry>I E D L++K++DG+L  EV + R E</entry><entry /></row><row><entry>Sbjct:</entry><entry>421</entry><entry>IEEQDRLEIKLKDGVLTCEVLEKRGE</entry><entry>446</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 275&gt; which encodes the amino acid sequence &lt;SEQ ID 276&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00295" num="00295"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3275(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00296" num="00296"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 321/446 (71%), Positives = 386/446 (85%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSDYLSVSTLTKYLKLKFDKDPYLERVYLTGQVSNFRRRPNHQYFSLKDDKSVIQATMWS</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+DYL+V+ LTKYLKLKFD+DPYLERVYLTGQVSNFR+RP HQYFSLKD+ +VIQATMW+</entry><entry /></row><row><entry>Sbjct:</entry><entry>6</entry><entry>MADYLTVTHLTKYLKLKFDRDPYLERVYLTGQVSNFRKRPTHQYFSLKDESAVIQATMWA</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GHFKKLGFELEEGMKVNVVGRVQLYEPSGSYSIIVEKAEPDGIGALAIQFEQLKKKLSQA</entry><entry>120</entry></row><row><entry /><entry /><entry>G +KKLGF+LEEGMK+NV+GRVQLYEPSGSYSI++EKAEPDGIGALA+QFEQLKKKL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>66</entry><entry>GVYKKLGFDLEEGMKINVIGRVQLYEPSGSYSIVIEKAEPDGIGALALQFEQLKKKLTAE</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GYFDDRHKQLIPQFVRKIGVVTSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGEGAAQE</entry><entry>180</entry></row><row><entry /><entry /><entry>GYF+ +HKQ +PQFV KIGV+TSPSGAVIRDIITTVSRRFPGVEILLFPTKVQG+GAAQE</entry><entry /></row><row><entry>Sbjct:</entry><entry>126</entry><entry>GYFEQKHKQPLPQFVSKIGVITSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGDGAAQE</entry><entry>185</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>IAQTIALANEKKDLDLLIVGRGGGSIEDLWAFNEECVVEAIFESRLPVISSVGHETDTTL</entry><entry>240</entry></row><row><entry /><entry /><entry>+   I  AN+++DLDLLIVGRGGGSIEDLWAFNEE VV+AIFES+LPVISSVGHETDTTL</entry><entry /></row><row><entry>Sbjct:</entry><entry>186</entry><entry>VVANIRRANQREDLDLLIVGRGGGSIEDLWAFNEEIVVQAIFESQLPVISSVGHETDTTL</entry><entry>245</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>ADFVADRRAATPTAAAELATPVTKIDILSWITERENRMYQSSLRLIRTKEERLQKSKQSV</entry><entry>300</entry></row><row><entry /><entry /><entry>ADFVADRRAATPTAAAELATP+TK D++SWI ER+NR YQ+ LR I+ ++E + K  QSV</entry><entry /></row><row><entry>Sbjct:</entry><entry>246</entry><entry>ADFVADRRAATPTAAAELATPITKTDLMSWIVERQNRSYQACLRRIKQRQEWVDKLSQSV</entry><entry>305</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>IFRQPERLYDGFLQKLDNLNQQLTYSMRDKLQTVRQKQGLLHQKLQGIDLKQRIHIYQER</entry><entry>360</entry></row><row><entry /><entry /><entry>IFRQPERLYD +LQK+D L+  L  +M+D+L + ++ +  L   L    L+ +I  YQ+R</entry><entry /></row><row><entry>Sbjct:</entry><entry>306</entry><entry>IFRQPERLYDAYLQKIDRLSMTLMNTMKDRLSSAKENKVQLDHALANSQLQTKIERYQDR</entry><entry>365</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>VVQSRRLLSSTMTSQYDSKLARFEKAQDALISLDSSRIVARGYAIIEKNHTLVSTTNGIN</entry><entry>420</entry></row><row><entry /><entry /><entry>V  ++RLL + M SQYDS+LARFEKAQDAL+SLD+SRI+ARGYA+IEKN  LV++ + I</entry><entry /></row><row><entry>Sbjct:</entry><entry>366</entry><entry>VATAKRLLMANMASQYDSQLARFEKAQDALLSLDASRIIARGYAMIEKNQALVASVSQIT</entry><entry>425</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>EGDHLQVKMQDGLLEVEVKDVRQENI</entry><entry>446</entry></row><row><entry /><entry /><entry>+GD L +KM+DG L+VEVKDV+ ENI</entry><entry /></row><row><entry>Sbjct:</entry><entry>426</entry><entry>KGDQLTIKMRDGQLDVEVKDVKNENI</entry><entry>451</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 83

A DNA sequence (GBSx0083) was identified in <i>S. agalactiae </i>&lt;SEQ ID 277&gt; which encodes the amino acid sequence &lt;SEQ ID 278&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00297" num="00297"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 33</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2913(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00298" num="00298"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAG07429 GB:AE004821 exodeoxyribonuclease VII small subunit</entry><entry /></row><row><entry>[<i>Pseudomonas aeruginosa</i>]</entry></row><row><entry>Identities = 26/66 (39%), Positives = 51/66 (76%), Gaps = 2/66 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSDKKT--FEENLQELETIVSRLETGDVALEDAIAEFQKGMLISKELQRTLKEAEETLVK</entry><entry>58</entry><entry /></row><row><entry /><entry /><entry>M+ KKT  FE++L EL+T+V RLE+G+++LE+++  F++G+ +++E Q +L +AE+ +</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MARKKTLDFEQSLTELQTLVERLESGELSLEESLGAFEQGIRLTRECQTSLSQAEQKVQI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>59</entry><entry>VMQADG</entry><entry>64</entry></row><row><entry /><entry /><entry>+++ DG</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LLERDG</entry><entry>66</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 279&gt; which encodes the amino acid sequence &lt;SEQ ID 280&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00299" num="00299"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2796(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00300" num="00300"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 55/70 (78%), Positives = 65/70 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSDKKTFEENLQELETIVSRLETGDVALEDAIAEFQKGMLISKELQRTLKEAEETLVKVM</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MS  KTFEENLQ+LETIV++LE GDV LE+AI+EFQKGML+SKELQ+TL+ AE+TLVKVM</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKTKTFEENLQDLETIVNKLENGDVPLEEAISEFQKGMLLSKELQKTLQAAEKTLVKVM</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QADGTEVEMD</entry><entry>70</entry></row><row><entry /><entry /><entry>QADGTEV+MD</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QADGTEVDMD</entry><entry>70</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 84

A DNA sequence (GBSx0084) was identified in <i>S. agalactiae </i>&lt;SEQ ID 281&gt; which encodes the amino acid sequence &lt;SEQ ID 282&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00301" num="00301"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2614(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00302" num="00302"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAA25265 GB: AB003187 farnesyl diphosphate synthase [<i>Micrococcus</i></entry><entry /></row><row><entry><i>luteus</i>]</entry></row><row><entry>Identities = 126/258 (48%), Positives = 175/258 (66%), Gaps = 2/258 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>27</entry><entry>LIKAILYSVDGGGKRIRPRILLEILEGFGVELIDGHYDVAAALEMIHTGSLIHDDLPAMD</entry><entry>86</entry><entry /></row><row><entry /><entry /><entry>L +AI YS+  GGKRIRP ++L  L+  G    DG      ALEMIHT SLIHDDLPAMD</entry></row><row><entry>Sbjct:</entry><entry>31</entry><entry>LHEAINYSLSAGGKRIRPLLVLTTLDSLGGNAHDG-LPFGIALEMIHTYSLIHDDLPAMD</entry><entry>89</entry></row><row><entry /></row><row><entry>Query:</entry><entry>87</entry><entry>NDDFRRGRLTNHKKFDEATAVLAGDSLFLDPFDLVVKAGFKADVTVRLIELLSMSAGSFG</entry><entry>146</entry></row><row><entry /><entry /><entry>NDD+RRG+LTNHK+FDEATA+LAGD+L  D F  ++     A++ + LI LLS ++GS G</entry></row><row><entry>Sbjct:</entry><entry>90</entry><entry>NDDYRRGKLTNHKRFDEATAILAGDALLTDAFQCILNTQLNAEIKLSLINLLSTASGSNG</entry><entry>149</entry></row><row><entry /></row><row><entry>Query:</entry><entry>147</entry><entry>MVGGQMLDMKGENKVLSIDDLSLIHINKTGRLLAYPFVAAGILAEKSEEVKGKLHQAGLL</entry><entry>206</entry></row><row><entry /><entry /><entry>MV GQMLDM+GE+K L++++L  IHI+KTG L+    V+AGI+   ++    +L+  G</entry></row><row><entry>Sbjct:</entry><entry>150</entry><entry>MVYGQMLDMQGEHKTLTLNELERIHIHKTGELIRAAIVSAGIIMNFNDAQIEQLNIIGKN</entry><entry>209</entry></row><row><entry /></row><row><entry>Query:</entry><entry>207</entry><entry>IGHAFQVRDDILDVTASFEELGKTPNKDIVAEKTTYPNLLGLDKSQEILDDTLKKAQAIF</entry><entry>266</entry></row><row><entry /><entry /><entry>+G  FQ++DDILDV  SFE +GKT   D+  +K+TY +LLGL+ S+++L+D L +</entry></row><row><entry>Sbjct:</entry><entry>210</entry><entry>VGLMFQIKDDILDVEGSFENIGKTVGSDLNNDKSTYVSLLGLEASKQLLNDKLTETYDAL</entry><entry>269</entry></row><row><entry /></row><row><entry>Query:</entry><entry>267</entry><entry>QNLEKKANFNARKIIDII</entry><entry>284</entry></row><row><entry /><entry /><entry>+ L+   N N + +I  I</entry></row><row><entry>Sbjct:</entry><entry>270</entry><entry>KTLQ-PINDNLKTLITYI</entry><entry>286</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 283&gt; which encodes the amino acid sequence &lt;SEQ ID 284&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00303" num="00303"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3887(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00304" num="00304"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 192/289 (66%), Positives = 237/289 (81%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>MVTIEKIDEAIHRYYKQTHSVVSPDLIKAILYSVDGGGKRIRPRILLEILEGFGVELIDG</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>M  + +IDEAI RYYK T + VS +LI AILYSVD GGKRIRP ILLE++EGFGV L +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MDKLARIDEAIRRYYKTTSNGVSEELIDAILYSVDSGGKRIRPLILLEMIEGFGVSLQNA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>HYDVAAALEMIHTGSLIHDDLPAMDNDDFRRGRLTNHKKFDEATAVLAGDSLFLDPFDLV</entry><entry>121</entry></row><row><entry /><entry /><entry>H+D+AAALEMIHTGSLIHDDLPAMDNDD+RRGRLTNHK+F EATA+LAGDSLFLDPF L+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>HFDLAAALEMIHTGSLIHDDLPAMDNDDYRRGRLTNHKQFGEATAILAGDSLFLDPFGLI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>VKAGFKADVTVRLIELLSMSAGSFGMVGGQMLDMKGENKVLSIDDLSLIHINKTGRLLAY</entry><entry>181</entry></row><row><entry /><entry /><entry> +A   ++V V LI+ LS+++G+FGMVGGQMLDMKGEN+ LS+  LSLIH+NKTG+LLA+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>AQAELNSEVKVALIQELSLASGTFGMVGGQMLDMKGENQALSLPQLSLIHLNKTGKLLAF</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>PFVAAGILAEKSEEVKGKLHQAGLLIGHAFQVRDDILDVTASFEELGKTPNKDIVAEKTT</entry><entry>241</entry></row><row><entry /><entry /><entry>PF AA ++ E++  V+ +L QAG+LIGHAFQ+RDDILDVTASFE+LGKTP KD+ AEK T</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>PFKAAALITEQAMTVRQQLEQAGMLIGHAFQIRDDILDVTASFEDLGKTPKKDLFAEKAT</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>YPNLLGLDKSQEILDDTLKKAQAIFQNLEKKANFNARKIIDIIEGLRLN</entry><entry>290</entry></row><row><entry /><entry /><entry>YP+LLGL+ S ++L ++L +A  IFQ LE    F  + I  +IEGLRLN</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YPSLLGLEASYQLLTESLDQALTIFQTLESDVGFKPQIITKLIEGLRLN</entry><entry>289</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 85

A DNA sequence (GBSx0085) was identified in <i>S. agalactiae </i>&lt;SEQ ID 285&gt; which encodes the amino acid sequence &lt;SEQ ID 286&gt;. This protein is predicted to be hemolysin-like protein (tly). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00305" num="00305"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.75</entry><entry>Transmembrane</entry><entry>152-168 (151-168)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1298(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00306" num="00306"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06497 GB: AP001516 hemolysin-like protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 162/270 (60%), Positives = 202/270 (74%), Gaps = 3/270 (1%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KERVDVLAYKQGLFDTREQAKRGVMAGMVINVINGERYDKPGEKVADDTELKLKGEKLKY</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>KERVDVL  ++GL +TRE+AKR +MAG+V +    ER DKPG KV  DT L +KGE L Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>4</entry><entry>KERVDVLLVERGLMETREKAKRSIMAGLVFS--GHERVDKPGLKVDRDTPLSVKGEVLPY</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>VSRGGLKLEKALQVFEISVADKLTIDIGASTGGFTDVMLQSGARLVYAVDVGTNQLVWKL</entry><entry>122</entry></row><row><entry /><entry /><entry>VSRGGLKLEKA++ F++ + D++ +DIGASTGGFTD  LQ+GA  VYAVDVG NQL WKL</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>VSRGGLKLEKAIRAFDLHLTDRVVLDIGASTGGFTDCALQNGATFVYAVDVGYNQLAWKL</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>RQDHRVRSMEQYNFRYAQKEDFKEGLPEFASIDVSFISLNLILPALKEILVDGGQVVALI</entry><entry>182</entry></row><row><entry /><entry /><entry>RQD RV  ME+ NFRY + E  + GLP  A+IDVSFISL LILP LK +L++   VVAL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>RQDERVVVMERTNFRYLKPEVLERGLPNMATIDVSFISLKLILPVLKTMLLENSDVVALV</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>KPQFEAGREQIGKNGIVKDKLVHEKVLTTVTNFTKDYGYTVKHLDFSPIQGGHGNIEFLM</entry><entry>242</entry></row><row><entry /><entry /><entry>KPQFEAGRE++GK GIV+DK VH+KVL+T+  F    GY V  LDFSPI GG GNIEFL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>KPQFEAGREEVGKKGIVRDKSVHQKVLSTIVEFALKEGYAVGGLDFSPITGGEGNIEFLL</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>HLQKCQDPQNLV-LDQIQDVIEKAHKEFKK</entry><entry>271</entry></row><row><entry /><entry /><entry>HL   +D ++ +  + I+D +E+AH E KK</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>HLMWRKDKESFISQEMIRDTVERAHLELKK</entry><entry>271</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 287&gt; which encodes the amino acid sequence &lt;SEQ ID 288&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00307" num="00307"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.92</entry><entry>Transmembrane</entry><entry>150-166 (149-168)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2168(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00308" num="00308"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06497 GB: AP001516 hemolysin-like protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 156/270 (57%), Positives = 196/270 (71%), Gaps = 3/270 (1%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KERVDVLAYKQGLFETREQAKRGVMAGLVVSVINGQRYDKPGDKIDDGTELKLKGEKLKY</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>KERVDVL  ++GL ETRE+AKR +MAGLV S    +R DKPG K+D  T L +KGE L Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>4</entry><entry>KERVDVLLVERGLMETREKAKRSIMAGLVFS--GHERVDKPGLKVDRDTPLSVKGEVLPY</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>VSRGGLKLEKGLHVFGVSVANQIGIDIGASTGGFTDVMLQDGAKLVYAVDVGTNQLVWKL</entry><entry>122</entry></row><row><entry /><entry /><entry>VSRGGLKLEK +  F + + +++ +DIGASTGGFTD  LQ+GA  VYAVDVG NQL WKL</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>VSRGGLKLEKAIRAFDLHLTDRVVLDIGASTGGFTDCALQNGATFVYAVDVGYNQLAWKL</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>RQDPRVRSMEQYNFRYAQPEDFNEGQPVFASIDVSFISLSLILPALHNVLSDQGQVIALI</entry><entry>182</entry></row><row><entry /><entry /><entry>RQD RV  ME+ NFRY +PE    G P  A+IDVSFISL LILP L  +L +   V+AL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>RQDERVVVMERTNFRYLKPEVLERGLPNMATIDVSFISLKLILPVLKTMLLENSDVVALV</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>KPQFEAGREQIGKKGIVKDKQIHEKVIQKVMDFASGYGFTVKGLDFSPIQGGHGNIEFLA</entry><entry>242</entry></row><row><entry /><entry /><entry>KPQFEAGRE++GKKGIV+DK +H+KV+  +++FA   G+ V GLDFSPI GG GNIEFL</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>KPQFEAGREEVGKKGIVRDKSVHQKVLSTIVEFALKEGYAVGGLDFSPITGGEGNIEFLL</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>HLAKSQTPET-LAPHLIQKVVAKAHKEFEK</entry><entry>271</entry></row><row><entry /><entry /><entry>HL   +  E+ ++  +I+  V +AH E +K</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>HLMWRKDKESFISQEMIRDTVERAHLELKK</entry><entry>271</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00309" num="00309"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 214/275 (77%), Positives = 238/275 (85%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAKERVDVLAYKQGLFDTREQAKRGVMAGMVINVINGERYDKPGEKVADDTELKLKGEKL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M KERVDVLAYKQGLF+TREQAKRGVMAG+V++VING+RYDKPG+K+ D TELKLKGEKL</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MPKERVDVLAYKQGLFETREQAKRGVMAGLVVSVINGQRYDKPGDKIDDGTELKLKGEKL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KYVSRGGLKLEKALQVFEISVADKLTIDIGASTGGFTDVMLQSGARLVYAVDVGTNQLVW</entry><entry>120</entry></row><row><entry /><entry /><entry>KYVSRGGLKLEK L VF +SVA+++ IDIGASTGGFTDVMLQ GA+LVYAVDVGTNQLVW</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KYVSRGGLKLEKGLHVFGVSVANQIGIDIGASTGGFTDVMLQDGAKLVYAVDVGTNQLVW</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>KLRQDHRVRSMEQYNFRYAQKEDFKEGLPEFASIDVSFISLNLILPALKEILVDGGQVVA</entry><entry>180</entry></row><row><entry /><entry /><entry>KLRQD RVRSMEQYNFRYAQ EDF EG P FASIDVSFISL+LILPAL  +L D GQV+A</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>KLRQDPRVRSMEQYNFRYAQPEDFNEGQPVFASIDVSFISLSLILPALHNVLSDQGQVIA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LIKPQFEAGREQIGKNGIVKDKLVHEKVLTTVTNFTKDYGYTVKHLDFSPIQGGHGNIEF</entry><entry>240</entry></row><row><entry /><entry /><entry>LIKPQFEAGREQIGK GIVKDK +HEKV+  V +F   YG+TVK LDFSPIQGGHGNIEF</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LIKPQFEAGREQIGKKGIVKDKQIHEKVIQKVMDFASGYGFTVKGLDFSPIQGGHGNIEF</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>LMHLQKCQDPQNLVLDQIQDVIEKAHKEFKKNEEE</entry><entry>275</entry></row><row><entry /><entry /><entry>L HL K Q P+ L    IQ V+ KAHKEF+K+E+E</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LAHLAKSQTPETLAPHLIQKVVAKAHKEFEKHEKE</entry><entry>275</entry></row></tbody></tgroup></table></tables>

SEQ ID 286 (GBS310) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 57</figref> (lane 3; MW 34 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 61</figref> (lane 4; MW 58.8 kDa).

The GBS310-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 210</figref>, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 282</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 86

A DNA sequence (GBSx0086) was identified in <i>S. agalactiae </i>&lt;SEQ ID 289&gt; which encodes the amino acid sequence &lt;SEQ ID 290&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00310" num="00310"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1966(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00311" num="00311"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA09426 GB: AJ010954 arginine repressor [<i>Bacillus</i></entry><entry /></row><row><entry><i>stearothermophilus</i>]</entry></row><row><entry>Identities = 49/153 (32%), Positives = 84/153 (54%), Gaps = 4/153 (2%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKKSERLNLIKQIVLNHAVETQHELLRRLEAYGVTLTQATISRDMNEIGIIKVPSAKGRY</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M K +R   I++I++NH +ETQ EL+  L+  G  +TQAT+SRD+ E+ ++KVP A GRY</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNKGQRHIKIREIIMNHEIETQDELVDMLKKAGFNVTQATVSRDIKELQLVKVPMANGRY</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IYGLSNENDPIFTTAVAKPIKTSILSISDKLLGLEQFININVIPGNSQLIKTFIMSHCQE</entry><entry>120</entry></row><row><entry /><entry /><entry> Y L   +D  F     + +K +++    KL G    + +  +PGN+  I   + +</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KYSL--PSDQRFNP--TQKLKRALMDAFVKLDGSGNLLVLKTLPGNAHAIGVLLDNLDWN</entry><entry>116</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HIFSLTADDNSLLLIAKSEADADHIRQSMIAML</entry><entry>153</entry></row><row><entry /><entry /><entry> I      D++ L+I ++  DA+ +   ++ ML</entry><entry /></row><row><entry>Sbjct:</entry><entry>117</entry><entry>EIVGTICGDDTCLIICRTAEDAEKVSGQLLGML</entry><entry>149</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 291&gt; which encodes the amino acid sequence &lt;SEQ ID 292&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00312" num="00312"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1717(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00313" num="00313"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 87/154 (56%), Positives = 118/154 (76%), Gaps = 1/154 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKKSERLNLIKQIVLNHAVETQHELLRRLEAYGVTLTQATISRDMNEIGIIKVPSARGRY</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKKSERL LIK++VL H +ETQH+LLR L  +G+ LTQATISRDMNEIGI+K+PS  GRY</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>MKKSERLELIKKMVLTHPIETQHDLLRLLAEHGLELTQATISRDMNEIGIVKIPSGSGRY</entry><entry>71</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IYGLSNENDPIFTTAVAKPIKTSILSISDKLLGLEQFININVIPGNSQLIKTFIMSHCQE</entry><entry>120</entry></row><row><entry /><entry /><entry>IYGLS ++         + IK++IL++SDK  GLEQ + + V+PGNS+LIK ++++   +</entry></row><row><entry>Sbjct:</entry><entry>72</entry><entry>IYGLSQDSGKKIVQG-PRSIKSTILAVSDKTKGLEQHLYLKVVPGNSKLIKRYLLADFSK</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HIFSLTADDNSLLLIAKSEADADHIRQSMIAMLE</entry><entry>154</entry></row><row><entry /><entry /><entry> IFSL ADD+SLLLIAKS ++AD IRQ ++  ++</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>AIFSLIADDDSLLLIAKSPSEADMIRQEILLWMQ</entry><entry>164</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 87

A DNA sequence (GBSx0088) was identified in <i>S. agalactiae </i>&lt;SEQ ID 293&gt; which encodes the amino acid sequence &lt;SEQ ID 294&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00314" num="00314"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3339(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 88

A DNA sequence (GBSx0089) was identified in <i>S. agalactiae </i>&lt;SEQ ID 295&gt; which encodes the amino acid sequence &lt;SEQ ID 296&gt;. This protein is predicted to be DNA repair protein recn (recN). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00315" num="00315"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1651 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00316" num="00316"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14355 GB: Z99116 recN [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 244/567 (43%), Positives = 366/567 (64%), Gaps = 18/567 (3%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLLEISIKNFAIIEEISLNFETGMTVLTGETGAGKSIIIDAMNMMLGSRASVEVIRHGAN</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>ML E+SIKNFAIIEE++++FE G+TVLTGETGAGKSIIIDA+++++G R S E +R+G</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLAELSIKNFAIIEELTVSFERGLTVLTGETGAGKSIIIDAISLLVGGRGSSEFVRYGEA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KAEIEGFFSVEKNQSLVQLLEENGIELADELII-RREIFQNGRSVSRINGQMVNLSTLKA</entry><entry>119</entry></row><row><entry /><entry /><entry>KAE+EG F +E   ++ +  E GI+++DE+I+ RR+I  +G+SV R+NG++V +++L+</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KAELEGLFLLESGHPVLGVCAEQGIDVSDEMIVMRRDISTSGKSVCRVNGKLVTIASLRE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>VGHYLVDIYGQHDQEELMKPNMHILMLDEFGNTEFNVIKERYQSLFDAYRQLRKRVLDKQ</entry><entry>179</entry></row><row><entry /><entry /><entry>+G  L+DI+GQHD + LM+   H+ +LD+F   E     + YQ  +  Y +L K++</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IGRLLLDIHGQHDNQLLMEDENHLQLLDKFAGAEVESALKTYQEGYQRYVKLLKKLKQLS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>KNEQENKSRIEMLEFQIAEIESVALKSDEDQTLLKQRDKLMNHKNIADTLTNAYLMLDNE</entry><entry>239</entry></row><row><entry /><entry /><entry>++EQE    +++++FQ+ EIES  L+ +ED+ L ++R ++ N + I ++L NAY  L +E</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>ESEQEMAHCLDLIQFQLEEIESAKLELNEDEQLQEERQQISNFEKIYESLQNAYNALRSE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>EFSSLSNVRSAMNDLMALEEFDREYKDLSTNLSEAYYVIEEVTKRLGDVIDDLDFDAGLL</entry><entry>299</entry></row><row><entry /><entry /><entry>+   L  V  A   L  + + +   K +S ++S +YY++E+ T ++ +++D+L+FD   L</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>Q-GGLDWVGMASAQLEDISDINEPLKKMSESVSNSYYLLEDATFQMRNMLDELEFDPERL</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>QEIENRLDVINTITRKYGGDVNDVLDYFDNITKEYSLLTGSEESSDALEKELKILEHDLI</entry><entry>359</entry></row><row><entry /><entry /><entry>  IE RL+ I  + RKYG  V D+L+Y   I +E   +   +    +L+KEL  +  D+</entry><entry /></row><row><entry>Sbjct:</entry><entry>300</entry><entry>NYIETRLNEIKQLKRKYGATVEDILEYASKIEEEIDQIENRDSHLQSLKKELDSVGKDVA</entry><entry>359</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>ESANQLSLERHKLAKQLENEIKQELTELYMEKADFQVQFTKG----------------KF</entry><entry>403</entry></row><row><entry /><entry /><entry>  A  +S  R   AK+L +EI +EL  LYMEK+ F  +F                   +</entry><entry /></row><row><entry>Sbjct:</entry><entry>360</entry><entry>VEAANVSQIRKTWAKKLADEIHRELKSLYMEKSTFDTEFKVRTASRNEEAPLVNGQPVQL</entry><entry>419</entry></row><row><entry /></row><row><entry>Query:</entry><entry>404</entry><entry>NKEGNEIVEFYISTNPGEGFKPLVKVASGGELSRLMLAIKSAFSRKEDKTSIVFDEVDTG</entry><entry>463</entry></row><row><entry /><entry /><entry> ++G ++V+F ISTN GE  K L KVASGGELSR+MLAIKS FS  ++D TSI+FDEVDTG</entry><entry /></row><row><entry>Sbjct:</entry><entry>420</entry><entry>TEQGIDLVKFLISTNTGEPLKSLSKVASGGELSRVMLAIKSIFSSQQDVTSIIFDEVDTG</entry><entry>479</entry></row><row><entry /></row><row><entry>Query:</entry><entry>464</entry><entry>VSGRVAQAIAQKIHKIGSHGQVLAISHLAQVIAIADYQYFIEKISSDSSTVSTVRLLSYE</entry><entry>523</entry></row><row><entry /><entry /><entry>VSGRVAQAIA+KIHK+    QVL I+HL QV A+AD   +I K   D  T + V+ LS +</entry><entry /></row><row><entry>Sbjct:</entry><entry>480</entry><entry>VSGRVAQAIAEKIHKVSIGSQVLCITHLPQVAAMADTHLYIAKELKDGRTTTRVKPLSKQ</entry><entry>539</entry></row><row><entry /></row><row><entry>Query:</entry><entry>524</entry><entry>ERVEEIAKMLAGNNVTDTARTQAKELL</entry><entry>550</entry></row><row><entry /><entry /><entry>E+V EI + +AG  VTD  +  AKELL</entry><entry /></row><row><entry>Sbjct:</entry><entry>540</entry><entry>EKVAEIERSIAGVEVTDLTKRHAKELL</entry><entry>566</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 297&gt; which encodes the amino acid sequence &lt;SEQ ID 298&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00317" num="00317"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1215 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00318" num="00318"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 403/550 (73%), Positives = 472/550 (85%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLLEISIKNFAIIEEISLNFETGMTVLTGETGAGKSIIIDAMNMMLGSRASVEVIRHGAN</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MLLEISIKNFAII+EISLNFE GMTVLTGETGAGKSIIIDAMNMMLG+RAS EVIR GAN</entry><entry /></row><row><entry>Sbjct:</entry><entry>2</entry><entry>MLLEISIKNFAIIDEISLNFENGMTVLTGETGAGKSIIIDAMNMMLGARASTEVIRRGAN</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KAEIEGFFSVEKNQSLVQLLEENGIELADELIIRREIFQNGRSVSRINGQMVNLSTLKAV</entry><entry>120</entry></row><row><entry /><entry /><entry>KAEIEGFFSV+    LV  LE +GI + +ELIIRR+IF NGRSVSRINGQMVNL+TLK V</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>KAEIEGFFSVDATPELVACLESSGIAMEEELIIRRDIFANGRSVSRINGQMVNLATLKQV</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GHYLVDIYGQHDQEELMKPNMHILMLDEFGNTEFNVIKERYQSLFDAYRQLRKRVLDKQK</entry><entry>180</entry></row><row><entry /><entry /><entry>G +LVDI+GQHDQEELM+P +H  +LD FG+  F  +KE YQ +FD Y+ LR++V+DKQK</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>GQFLVDIHGQHDQEELMRPQLHQQILDAFGDKAFEQLKENYQLIFDRYKSLRRQVIDKQK</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>NEQENKSRIEMLEFQIAEIESVALKSDEDQTLLKQRDKLMNHKNIADTLTNAYLMLDNEE</entry><entry>240</entry></row><row><entry /><entry /><entry>NE+E+K RI+ML FQIAEIE+ AL   ED  L ++RD+LMNHK IADTLTNAY+MLDN++</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>NEKEHKDRIDMLAFQIAEIEAAALSRGEDDRLNQERDRLMNHKQIADTLTNAYVMLDNDD</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>FSSLSNVRSAMNDLMALEEFDREYKDLSTNLSEAYYVIEEVTKRLGDVIDDLDFDAGLLQ</entry><entry>300</entry></row><row><entry /><entry /><entry>FSSLSN+RS+MNDL+++E+FD EYK +ST++SEAYY++EEV+K+L D ID LDFD G LQ</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>FSSLSNIRSSMNDLLSIEQFDSEYKGMSTSISEAYYILEEVSKQLSDTIDQLDFDGGRLQ</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>EIENRLDVINTITRKYGGDVNDVLDYFDNITKEYSLLTGSEESSDALEKELKILEHDLIE</entry><entry>360</entry></row><row><entry /><entry /><entry>EIE RLD++N++TRKYGG+VNDVLDY+DNI KEY LLTG + SS  LE ELK LE  L+</entry><entry /></row><row><entry>Sbjct:</entry><entry>302</entry><entry>EIEFRLDILNSLTRKYGGNVNDVLDYYDNIVKEYQLLTGDDLSSGDLEAELKSLEKQLVA</entry><entry>361</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>SANQLSLERHKLAKQLENEIKQELTELYMEKADFQVQFTKGKFNKEGNEIVEFYISTNPG</entry><entry>420</entry></row><row><entry /><entry /><entry>+A++LS+ RH+LA+QLE EIK EL ELYMEKADF+V FT  KFN++GNE +EFYISTNPG</entry><entry /></row><row><entry>Sbjct:</entry><entry>362</entry><entry>AASELSVSRHQLAEQLEAEIKAELKELYMEKADFKVHFTTSKFNRDGNESLEFYISTNPG</entry><entry>421</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>EGFKPLVKVASGGELSRLMLAIKSAFSRKEDKTSIVFDEVDTGVSGRVAQAIAQKIHKIG</entry><entry>480</entry></row><row><entry /><entry /><entry>EGFKPLVKVASGGELSRLMLAIK+A SRKEDKTSIVFDEVDTGVSGRVAQAIAQKI+KIG</entry><entry /></row><row><entry>Sbjct:</entry><entry>422</entry><entry>EGFKPLVKVASGGELSRLMLAIKAAISRKEDKTSIVFDEVDTGVSGRVAQAIAQKIYKIG</entry><entry>481</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>SHGQVLAISHLAQVIAIADYQYFIEKISSDSSTVSTVRLLSYEERVEEIAKMLAGNNVTD</entry><entry>540</entry></row><row><entry /><entry /><entry> HGQVLAISHL QVIAIADYQYFI K S + STVS VRLL+ EERVEEIA M+AG ++T</entry><entry /></row><row><entry>Sbjct:</entry><entry>482</entry><entry>RHGQVLAISHLPQVIAIADYQYFISKESKEESTVSKVRLLTPEERVEEIASMIAGTDMTQ</entry><entry>541</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>TARTQAKELL</entry><entry>550</entry></row><row><entry /><entry /><entry> A TQA+ELL</entry><entry /></row><row><entry>Sbjct:</entry><entry>542</entry><entry>AALTQARELL</entry><entry>551</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 89

A DNA sequence (GBSx0090) was identified in <i>S. agalactiae </i>&lt;SEQ ID 299&gt; which encodes the amino acid sequence &lt;SEQ ID 300&gt;. This protein is predicted to be degV protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00319" num="00319"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>   INTEGRAL</entry><entry>Likelihood = −0.96</entry><entry>Transmembrane</entry><entry>246-262 (246-262)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1383 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00320" num="00320"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB07346 GB:AP001519 unknown conserved protein</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 93/277 (33%), Positives = 152/277 (54%), Gaps = 4/277 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKIKIVTDSSITIEPELIKELDITVVPLSVMIDGTLYSDNDLKAQGEFLNLMRGSKELP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+KI IVTDS+  + P+  KEL + VVPLSV+     Y +    +  +F   ++  ++LP</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTKIAIVTDSTAYLGPKRAKELGVIVVPLSVVFGEEAYQEEVELSSADFYERLKHEEKLP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KTSQPPVGVFAEIYEKLMNEGVEHIIAIHLTHTLSGTIE-ASRQGANIAGADVTVIDSTF</entry><entry>119</entry></row><row><entry /><entry /><entry> TSQP VG+F E +E+L  EG E +I+IHL+  +SGT + A   G+ + G +V   DS</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TTSQPAVGLFVETFERLAKEGFEVVISIHLSSKISGTYQSALTAGSMVEGIEVIGYDSGI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>TDQCQKFQVVEAAKLAKEGADLDTILARVEEVRQKSELFIGVSTLENLVKGGRIGRVTGL</entry><entry>179</entry></row><row><entry /><entry /><entry>+ + Q   V EAAKL KEGAD  TI+  ++EV++++     V  L +L +GGR+     +</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SCEPQANFVAEAAKLVKEGADPQTIIDHLDEVKKRTNALFVVHDLSHLHRGGRLNAAQLV</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>LSSLLNIKVIMELTNHELVPIVKGR-GLKTFSKWLDNFVESAQTRKIAEIGISYCGKADM</entry><entry>238</entry></row><row><entry /><entry /><entry>+ SLL IK I+   +  +VP+ K R   K +++  + F E A +    +  + +  + D</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VGSLLKIKPILHFEDGSIVPLEKVRTEKKAWARVKELFAEEASSASSVKATVIHANRLDG</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>239</entry><entry>ANNFREKL-AVLGAPISVLETGSIIQTHTGEDAFAV</entry><entry>273</entry></row><row><entry /><entry /><entry>A    +++        +S+   G +I TH GE +  +</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AEKLADEIRSQFSHVDVSISHFGPVIGTHLGEGSIGL</entry><entry>277</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 301&gt; which encodes the amino acid sequence &lt;SEQ ID 302&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00321" num="00321"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.54</entry><entry>Transmembrane</entry><entry>180-196 (180-196)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.16</entry><entry>Transmembrane</entry><entry>  21-37 (21-38)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1617(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00322" num="00322"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 197/279 (70%), Positives = 226/279 (80%), Gaps = 1/279 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKIKIVTDSSITIEPELIKELDITVVPLSVMIDGTLYSDNDLKAQGEFLNLMRGSKELP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  IKIVTDSSITIEPELIK LDITVVPLSVMID  LYSDNDLK +G FL+LM+ SK LP</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>MGTIKIVTDSSITIEPELIKALDITVVPLSVMIDSKLYSDNDLKEEGHFLSLMKASKSLP</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KTSQPPVGVFAEIYEKLMNEGVEHIIAIHLTHTLSGTIEASRQGANIAGADVTVIDSTFT</entry><entry>120</entry></row><row><entry /><entry /><entry>KTSQPPVG+FAE YE L+ +GV  I+AIHL+  LSGTIEASRQGA IA A VTV+DS FT</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>KTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFT</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DQCQKFQVVEAAKLAKEGADLDTILARVEEVRQKSELFIGVSTLENLVKGGRIGRVTGLL</entry><entry>180</entry></row><row><entry /><entry /><entry>DQ  KFQVVEAAK+AK GA L+ ILA V+ ++ K+EL+IGVSTLENLVKGGRIGRVTG+L</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>DQAMKFQVVEAAKMAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTGVL</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SSLLNIKVIMELTNHELVPIVKGRGLKTFSKWLDNFVESAQTRKIAEIGISYCGKADMAN</entry><entry>240</entry></row><row><entry /><entry /><entry>SSLLN+KV+M L N EL  +VKGRG KTF+KWLD+++     R IAEI ISY G+A +A</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>SSLLNVKVVMALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLAL</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>NFREKLAV-LGAPISVLETGSIIQTHTGEDAFAVMVRYE</entry><entry>278</entry></row><row><entry /><entry /><entry>  +E++A      ISVLETGSIIQTHTGE AFAVMVRYE</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>TLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVMVRYE</entry><entry>283</entry></row></tbody></tgroup></table></tables>

SEQ ID 300 (GBS113) was expressed in <i>E. coli </i>as a His-fusion product. Purified protein is shown in <figref idrefs="DRAWINGS">FIG. 201</figref>, lane 8.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 90

A DNA sequence (GBSx0092) was identified in <i>S. agalactiae </i>&lt;SEQ ID 307&gt; which encodes the amino acid sequence &lt;SEQ ID 308&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00323" num="00323"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00324" num="00324"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA72097 GB: Y11213 hypothetical protein [<i>Streptococcus thermophilus</i>]</entry><entry /></row><row><entry>Identities = 75/185 (40%), Positives = 116/185 (62%), Gaps = 3/185 (1%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>WKWAFLLLLAINLSFTAVIASRLIQVREPNTGKISTGVQDKVKVGTFTTNKSQLNKTIAL</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>WKW FL LLA+NL+  +V+  R++   E +   +  G     K+G ++ +K +L++++</entry><entry /></row><row><entry>Sbjct:</entry><entry>5</entry><entry>WKWLFLGLLALNLALISVVTVRIMTPVETSPVSLPKGA---TKIGKYSMSKEELDESLRG</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>YLKQYQTKKMNYKIYAASSSILFEGSYQLLGYEVPLYIYFEPYRLTNGAVQLKVTSFSVG</entry><entry>132</entry></row><row><entry /><entry /><entry>+ + Y T KM +K+   +S I+FE SY++LG+ VPLY+YF P    +GAV L+ +  S G</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>FAQDYSTDKMRFKVKVTNSKIVFESSYKVLGHAVPLYVYFTPLVSESGAVVLQESELSAG</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>133</entry><entry>TLPLPEKDVLQYIKSSYKLPNFVDIKPKKSVININLQDLKNKEGIYLKATAIDLVNDNFS</entry><entry>192</entry></row><row><entry /><entry /><entry>TL LP  D L  IK S KLP+++ I  KK  + +N+Q +KN +GI  +A + DLVND</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>TLKLPILDALNMIKRSTKLPDYIVIDSKKGKVILNIQSMKNDKGITARAQSFDLVNDRSE</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>193</entry><entry>FDIFK</entry><entry>197</entry></row><row><entry /><entry /><entry>FDI+K</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>FDIYK</entry><entry>186</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 309&gt; which encodes the amino acid sequence &lt;SEQ ID 310&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00325" num="00325"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00326" num="00326"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA72097 GB: Y11213 hypothetical protein [<i>Streptococcus thermophilus</i>]</entry><entry /></row><row><entry>Identities = 73/185 (39%), Positives = 112/185 (60%), Gaps = 3/185 (1%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>10</entry><entry>WKWSFLCLLAFNTAFLMVIASRLIQVREPESELIAKKPVKNIKIGTFVTTREQLNETVAS</entry><entry>69</entry><entry /></row><row><entry /><entry /><entry>WKW FL LLA N A + V+  R++   E     + K   K   IG +  ++E+L+E++</entry><entry /></row><row><entry>Sbjct:</entry><entry>5</entry><entry>WKWLFLGLLALNLALISVVTVRIMTPVETSPVSLPKGATK---IGKYSMSKEELDESLRG</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>70</entry><entry>YLKDYQTEKMSYKFYATSSSILFEGTYQLLGYEVPLYIYFQPHRLENGAVQLQVISFSVG</entry><entry>129</entry></row><row><entry /><entry /><entry>+ +DY T+KM +K   T+S I+FE +Y++LG+ VPLY+YF P   E+GAV LQ    S G</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>FAQDYSTDKMRFKVKVTNSKIVFESSYKVLGHAVPLYVYFTPLVSESGAVVLQESELSAG</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>130</entry><entry>TLPLPEKDVLQYLKSSYKLPSFVKVMPNQSAIVVNLQDIQNDAKVYLKAKKIDLFNDEIS</entry><entry>189</entry></row><row><entry /><entry /><entry>TL LP  D L  +K S KLP ++ +   +  +++N+Q ++ND  +  +A+  DL ND</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>TLKLPILDALNMIKRSTKLPDYIVIDSKKGKVILNIQSMKNDKGITARAQSFDLVNDRSE</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>190</entry><entry>FNIYK</entry><entry>194</entry></row><row><entry /><entry /><entry>F+IYK</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>FDIYK</entry><entry>186</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00327" num="00327"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 129/194 (66%), Positives = 155/194 (79%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>KTGRNLNFWKWAFLLLLAINLSFTAVIASRLIQVREPNTGKISTGVQDKVKVGTFTTNKS</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>K   NLN+WKW+FL LLA N +F  VIASRLIQVREP +  I+      +K+GTF T +</entry><entry /></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KKKSNLNWWKWSFLCLLAFNTAFLMVIASRLIQVREPESELIAKKPVKNIKIGTFVTTRE</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>QLNKTIALYLKQYQTKKMNYKIYAASSSILFEGSYQLLGYEVPLYIYFEPYRLTNGAVQL</entry><entry>124</entry></row><row><entry /><entry /><entry>QLN+T+A YLK YQT+KM+YK YA SSSILFEG+YQLLGYEVPLYIYF+P+RL NGAVQL</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>QLNETVASYLKDYQTEKMSYKFYATSSSILFEGTYQLLGYEVPLYIYFQPHRLENGAVQL</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>KVTSFSVGTLPLPEKDVLQYIKSSYKLPNFVDIKPKKSVININLQDLKNKEGIYLKATAI</entry><entry>184</entry></row><row><entry /><entry /><entry>+V SFSVGTLPLPEKDVLQY+KSSYKLP+FV + P +S I +NLQD++N   +YLKA  I</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>QVISFSVGTLPLPEKDVLQYLKSSYKLPSFVKVMPNQSAIVVNLQDIQNDAKVYLKAKKI</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>DLVNDNFSFDIFKK</entry><entry>198</entry></row><row><entry /><entry /><entry>DL ND  SF+I+KK</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>DLFNDEISFNIYKK</entry><entry>195</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

A related GBS gene &lt;SEQ ID 8487&gt; and protein &lt;SEQ ID 8488&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00328" num="00328"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 7</entry><entry /></row><row><entry>McG: Discrim Score: 7.47</entry></row><row><entry>GvH: Signal Score (−7.5): 2.42</entry></row><row><entry>     Possible site: 28</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry>ALOM program count: 0 value: 5.89 threshold: 0.0</entry></row><row><entry>PERIPHERAL Likelihood = 5.89 120</entry></row><row><entry>modified ALOM score: −1.68</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 308 (GBS20) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 4</figref> (lane 5; MW 25 kDa) and in <figref idrefs="DRAWINGS">FIG. 167</figref> (lane 12-14; MW 37 kDa—thioredoxin fusion). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 9</figref> (lane 7; MW 47.6 kDa). Purified Thio-GBS20-His is shown in <figref idrefs="DRAWINGS">FIG. 244</figref>, lane 12.

EXAMPLE 91

A DNA sequence (GBSx0093) was identified in <i>S. agalactiae </i>&lt;SEQ ID 311&gt; which encodes the amino acid sequence &lt;SEQ ID 312&gt;. This protein is predicted to be histone-like DNA-binding protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00329" num="00329"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2768(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9313&gt; which encodes amino acid sequence &lt;SEQ ID 9314&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00330" num="00330"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="259pt" align="left" /><colspec colname="2" colwidth="182pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD40810 GB: L40355 histone-like DNA-binding protein</entry><entry /></row><row><entry>[<i>Streptococcus mutans</i>]</entry></row><row><entry>Identities = 43/47 (91%), Positives = 46/47 (97%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="7pt" align="center" /><colspec colname="3" colwidth="203pt" align="left" /><colspec colname="4" colwidth="21pt" align="center" /><colspec colname="5" colwidth="182pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVFAAVADYLAEGEKVQLIG</entry><entry>47</entry><entry /></row><row><entry /><entry /><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVF+AV+ YLA+GEKVQLIG</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVFSAVSSYLAKGEKVQLIG</entry><entry>47</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 313&gt; which encodes the amino acid sequence &lt;SEQ ID 314&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00331" num="00331"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2834(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00332" num="00332"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="259pt" align="left" /><colspec colname="2" colwidth="182pt" align="left" /><tbody valign="top"><row><entry>Identities = 41/47 (87%), Positives = 44/47 (93%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="center" /><colspec colname="3" colwidth="203pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="182pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVFAAVADYLAEGEKVQLIG</entry><entry>47</entry><entry /></row><row><entry /><entry /><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVF+ +  +LAEGEKVQLIG</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MANKQDLIAKVAEATELTKKDSAAAVDAVFSTIEAFLAEGEKVQLIG</entry><entry>47</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 92

A DNA sequence (GBSx0094) was identified in <i>S. agalactiae </i>&lt;SEQ ID 315&gt; which encodes the amino acid sequence &lt;SEQ ID 316&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00333" num="00333"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2722(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9293&gt; which encodes amino acid sequence &lt;SEQ ID 9294&gt; was also identified. A further related GBS nucleic acid sequence &lt;SEQ ID 10793&gt; which encodes amino acid sequence &lt;SEQ ID 10794&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00334" num="00334"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD17886 GB: AF100456 hyaluronate-associated protein precursor</entry><entry /></row><row><entry>[<i>Streptococcus equi</i>]</entry></row><row><entry>Identities = 303/435 (69%), Positives = 360/435 (82%), Gaps = 1/435 (0%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MATKVDVSKDGLTYTATLRKGLKWSDGSKLTAKDFVYSWQRLVDPKTASQYAYLAVEGHV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+A KVDVS+DGLTYTATLR GLKWSDGS LTA+DFVYSWQR+VDPKTAS+YAYLA E H+</entry><entry /></row><row><entry>Sbjct:</entry><entry>87</entry><entry>LAEKVDVSEDGLTYTATLRDGLKWSDGSDLTAEDFVYSWQRMVDPKTASEYAYLATESHL</entry><entry>146</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LNADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIYYLAFTNFMPQKQEVVEKYGK</entry><entry>120</entry></row><row><entry /><entry /><entry> NA+ IN G+  DL+ LGVKA+G+ KV+ TL+ P+PQF   L+F+NF+PQK+  V+  GK</entry><entry /></row><row><entry>Sbjct:</entry><entry>147</entry><entry>KNAEDINSGKNPDLDSLGVKADGN-KVIFTLTEPAPQFKSLLSFSNFVPQKESFVKDAGK</entry><entry>205</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DYATTSKNTVYSGPYTVEGWNGSNGTFTLKKNKNYWDAKNVKTKEVRIQTVKKPDTAVQM</entry><entry>180</entry></row><row><entry /><entry /><entry>DY TTS+  +YSGPY V+ WNG++GTF L KNKNYWDAKNVKT+ V +QTVKKPDTAVQM</entry><entry /></row><row><entry>Sbjct:</entry><entry>206</entry><entry>DYGTTSEKQIYSGPYIVKDWNGTSGTFKLVKNKNYWDAKNVKTETVNVQTVKKPDTAVQM</entry><entry>265</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>YKRGELDAANISNTSAIYQANKNNKDVTDVLEATTAYMEYNTTGSVKGLDNVKIRRALNL</entry><entry>240</entry></row><row><entry /><entry /><entry>YK+G+LD ANIS TSAIY ANK +KDV  VLEATTAY+ YN TG+++GL+++KIR+ALNL</entry><entry /></row><row><entry>Sbjct:</entry><entry>266</entry><entry>YKQGKLDFANISGTSAIYNANKKHKDVVPVLEATTAYIVYNQTGAIEGLNSLKIRQALNL</entry><entry>325</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>ATNRKGVVQAAVDTGSKPAIAFAPTGLAKTPDGTDLAKYVAPGYEYNKTEAAKLFKEGLA</entry><entry>300</entry></row><row><entry /><entry /><entry>AT+RKG+V AAVDTGSKPA A  PTGLAK  DGTDL ++VAPGY+Y+  EAAKLFKEGLA</entry><entry /></row><row><entry>Sbjct:</entry><entry>326</entry><entry>ATDRKGIVSAAVDTGSKPATALVPTGLAKLSDGTDLTEHVAPGYKYDDKEAAKLFKEGLA</entry><entry>385</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>ESGLTKLKLTITADADAPAAKNSVDYIKSTWEAALPGLTVEEKFVTFKQRLEDSRKQNFD</entry><entry>360</entry></row><row><entry /><entry /><entry>E G   L +TITADADAPAAK++VDYIK TWE ALPGLTVEEKFV FKQRLED++ QNF+</entry><entry /></row><row><entry>Sbjct:</entry><entry>386</entry><entry>ELGKDALTITITADADAPAAKSAVDYIKETWETALPGLTVEEKFVPFKQRLEDTKNQNFE</entry><entry>445</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>IVVSLWGGDYPEGSTFYGLFKSDSQNNDGKFANKDYDAAYNKAISEDAMKPAESAKDYKE</entry><entry>420</entry></row><row><entry /><entry /><entry>+ V LWGGDYP+GSTFYGLFKS S  N GKF N DYDAAYNKA++ DA+    +A DYK</entry><entry /></row><row><entry>Sbjct:</entry><entry>446</entry><entry>VAVVLWGGDYPKGSTFYGLFKSGSAYNYGKFTNADYDAAYNKALTTDALNTDAAADDYKA</entry><entry>505</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>AEKILFEQGAYNPLY</entry><entry>435</entry></row><row><entry /><entry /><entry>AEK L++   YNPLY</entry><entry /></row><row><entry>Sbjct:</entry><entry>506</entry><entry>AEKALYDNALYNPLY</entry><entry>520</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8489&gt; and protein &lt;SEQ ID 8490&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00335" num="00335"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Lipop:Possible site:21 Crend:4</entry><entry /></row><row><entry>       Sequence Pattern:CGSK</entry></row><row><entry>SRCFLG:0</entry></row><row><entry>McG:Length of UR:19</entry></row><row><entry>     Peak Value of UR:2.34</entry></row><row><entry>     Net Charge of CR:3</entry></row><row><entry>McG:Discrim Score:5.94</entry></row><row><entry>GvH:Signal Score (−7.5):0.6</entry></row><row><entry>     Possible site:20</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry>Amino Acid Composition:calculated from 22</entry></row><row><entry>ALOM program count:0 value:5.14 threshold:0.0</entry></row><row><entry>   PERIPHERAL Likelihood = 5.14 166</entry></row><row><entry>modified ALOM score:−1.53</entry></row><row><entry>*** Reasoning Step:3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00336" num="00336"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP|4336671|gb|AAD17886.1||AF100456 hyaluronate-associated protein</entry><entry /></row><row><entry>precursor {<i>Streptococcus equi</i>}</entry></row><row><entry>Score = 721 bits (1840), Expect = 0.0</entry></row><row><entry>Identities = 354/515 (68%), Positives = 417/515 (80%), Gaps = 2/515 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>KNWRRVGVGVLTLASVATLAACGSK-SASQDSNGAINWAIPTEINTLDLSKVTDTYSNLA</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>K  +R+G+  +TLASVA L ACG+K SAS D    INW  PTEI TLD+SK TDTYS LA</entry><entry /></row><row><entry>Sbjct:</entry><entry>7</entry><entry>KACKRLGLAAVTLASVAALMACGNKQSASTDKKSEINWYTPTEIITLDISKNTDTYSALA</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>IGNSSSNFLRLDKDGKTRPDLATKVDVSKDGLTYTATLRKGLKWSDGSKLTAKDFVYSWQ</entry><entry>119</entry></row><row><entry /><entry /><entry>IGNS SN LR D  GK +PDLA KVDVS+DGLTYTATLR GLKWSDGS LTA+DFVYSWQ</entry><entry /></row><row><entry>Sbjct:</entry><entry>67</entry><entry>IGNSGSNLLRADAKGKLQPDLAEKVDVSEDGLTYTATLRDGLKWSDGSDLTAEDFVYSWQ</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>RLVDPKTASQYAYLAVEGHVLNADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIY</entry><entry>179</entry></row><row><entry /><entry /><entry>R+VDPKTAS+YAYLA E H+ NA+ IN G+  DL+ LGVKA+G+ KV+ TL+ P+PQF</entry><entry /></row><row><entry>Sbjct:</entry><entry>127</entry><entry>RMVDPKTASEYAYLATESHLKNAEDINSGKNPDLDSLGVKADGN-KVIFTLTEPAPQFKS</entry><entry>185</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>YLAFTNFMPQKQEVVEKYGKDYATTSKNTVYSGPYTVEGWNGSNGTFTLKKNKNYWDAKN</entry><entry>239</entry></row><row><entry /><entry /><entry> L+F+NF+PQK+  V+  GKDY TTS+  +YSGPY V+ WNG++GTF L KNKNYWDAKN</entry><entry /></row><row><entry>Sbjct:</entry><entry>186</entry><entry>LLSFSNFVPQKESFVKDAGKDYGTTSEKQIYSGPYIVKDWNGTSGTFKLVKNKNYWDAKN</entry><entry>245</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>VKTKEVRIQTVKKPDTAVQMYKRGELDAANISNTSAIYQANKNNKDVTDVLEATTAYMEY</entry><entry>299</entry></row><row><entry /><entry /><entry>VKT+ V +QTVKKPDTAVQMYK+G+LD ANIS TSAIY ANK +KDV  VLEATTAY+ Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>246</entry><entry>VKTETVNVQTVKKPDTAVQMYKQGKLDFANISGTSAIYNANKKHKDVVPVLEATTAYIVY</entry><entry>305</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>NTTGSVKGLDNVKIRRALNLATNRKGVVQAAVDTGSKPAIAFAPTGLAKTPDGTDLAKYV</entry><entry>359</entry></row><row><entry /><entry /><entry>N TG+++GL+++KIR+ALNLAT+RKG+V AAVDTGSKPA A  PTGLAK  DGTDL ++V</entry><entry /></row><row><entry>Sbjct:</entry><entry>306</entry><entry>NQTGAIEGLNSLKIRQALNLATDRKGIVSAAVDTGSKPATALVPTGLAKLSDGTDLTEHV</entry><entry>365</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>APGYEYNKTEAAKLFKEGLAESGLTKLKLTITADADAPAAKNSVDYIKSTWEAALPGLTV</entry><entry>419</entry></row><row><entry /><entry /><entry>APGY+Y+  EAAKLFKEGLAE G   L +TITADADAPAAK++VDYIK TWE ALPGLTV</entry><entry /></row><row><entry>Sbjct:</entry><entry>366</entry><entry>APGYKYDDKEAAKLFKEGLAELGKDALTITITADADAPAAKSAVDYIKETWETALPGLTV</entry><entry>425</entry></row><row><entry /></row><row><entry>Query:</entry><entry>420</entry><entry>EEKFVTFKQRLEDSRKQNFDIVVSLWGGDYPEGSTFYGLFKSDSQNNDGKFANKDYDAAY</entry><entry>479</entry></row><row><entry /><entry /><entry>EEKFV FKQRLED++ QNF++ V LWGGDYP+GSTFYGLFKS S  N GKF N DYDAAY</entry><entry /></row><row><entry>Sbjct:</entry><entry>426</entry><entry>EEKFVPFKQRLEDTKNQNFEVAVVLWGGDYPKGSTFYGLFKSGSAYNYGKFTNADYDAAY</entry><entry>485</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>NKAISEDAMKPAESAKDYKEAEKILFEQGAYNPLY</entry><entry>514</entry></row><row><entry /><entry /><entry>NKA++ DA+    +A DYK AEK L++   YNPLY</entry><entry /></row><row><entry>Sbjct:</entry><entry>486</entry><entry>NKALTTDALNTDAAADDYKAAEKALYDNALYNPLY</entry><entry>520</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 317&gt; which encodes the amino acid sequence &lt;SEQ ID 318&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00337" num="00337"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00338" num="00338"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 114/428 (26%), Positives = 185/428 (42%), Gaps = 63/428 (14%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>VSKDGLTYTATLRKGLKW--SDGSK---LTAKDFVYSWQRLVDPKTASQYAYLAVEGHVL</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>VSKDGLTYT TLR G+ W  +DG +   +TA+DFV   +  VD K+ + Y    VE  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>92</entry><entry>VSKDGLTYTYTLRDGVSWYTADGEEYAPVTAEDFVTGLKHAVDDKSDALY---VVEDSIK</entry><entry>148</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>NADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIYYLAFTNFMPQKQEVVEKYGKD</entry><entry>121</entry></row><row><entry /><entry /><entry>N      G E D  ++GVKA  D  V  TL+ P   +     ++   P   + ++  GKD</entry><entry /></row><row><entry>Sbjct:</entry><entry>149</entry><entry>NLKAYQNG-EVDFKEVGVKALDDKTVQYTLNKPESYWNSKTTYSVLFPVNAKFLKSKGKD</entry><entry>207</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>YATTSKNTV-YSGPYTVEGWNGSNGTFTLKKNKNYWDAKNVKTKEVRI--QTVKKPDTAV</entry><entry>178</entry></row><row><entry /><entry /><entry>+ TT  +++  +G Y +  +  S  +    KN+NYWDAKNV  + V++       P +</entry><entry /></row><row><entry>Sbjct:</entry><entry>208</entry><entry>FGTTDPSSILVNGAYFLSAFT-SKSSMEFHKNENYWDAKNVGIESVKLTYSDGSDPGSFY</entry><entry>266</entry></row><row><entry /></row><row><entry>Query:</entry><entry>179</entry><entry>QMYKRGELDAANISNTSAIYQANKNN--KDVT-DVLEATTAYMEYNTT------------</entry><entry>223</entry></row><row><entry /><entry /><entry>+ + +GE   A +      Y++ K N   ++T  +L     ++ +N</entry><entry /></row><row><entry>Sbjct:</entry><entry>267</entry><entry>KNFDKGEFSVARLYPNDPTYKSAKKNYADNITYGMLTGDIRHLTWNLNRTSFKNTKKDPA</entry><entry>326</entry></row><row><entry /></row><row><entry>Query:</entry><entry>224</entry><entry>---GSVKGLDNVKIRRALNLATNRKGVVQAAVDTGSKPA----IAFAPT--GLAKTPDGT</entry><entry>274</entry></row><row><entry /><entry /><entry>      K L+N   R+A+  A +R           +K      +   PT   + ++  G+</entry><entry /></row><row><entry>Sbjct:</entry><entry>327</entry><entry>QQDAGKKALNNKDFRQAIQFAFDRASFQAQTAGQDAKTKALRNMLVPPTFVTIGESDFGS</entry><entry>386</entry></row><row><entry /></row><row><entry>Query:</entry><entry>275</entry><entry>DLAKYVAP-GYE-------------YNKTEAAKLF---KEGLAESGLT-KLKLTITADAD</entry><entry>316</entry></row><row><entry /><entry /><entry>++ K +A  G E             YN  +A   F   KE L   G+T  ++L    D</entry><entry /></row><row><entry>Sbjct:</entry><entry>387</entry><entry>EVEKEMAKLGDEWKDVNLADAQDGFYNPEKAKAEFAKAKEALTAEGVTFPVQLDYPVDQA</entry><entry>446</entry></row><row><entry /></row><row><entry>Query:</entry><entry>317</entry><entry>APAAKNSVDYIKSTWEAALPGLTV-----EEKFVTFKQR---LEDSRKQNFDIVVSLWGG</entry><entry>368</entry></row><row><entry /><entry /><entry>  A        K + EA+L    V      E +  T + +    E   +Q++DI+ S WG</entry><entry /></row><row><entry>Sbjct:</entry><entry>447</entry><entry>NAATVQEAQSFKQSVEASLGKENVIVNVLETETSTHEAQGFYAETPEQQDYDIISSWWGP</entry><entry>506</entry></row><row><entry /></row><row><entry>Query:</entry><entry>369</entry><entry>DYPEGSTF</entry><entry>376</entry></row><row><entry /><entry /><entry>DY +  T+</entry><entry /></row><row><entry>Sbjct:</entry><entry>507</entry><entry>DYQDPRTY</entry><entry>514</entry></row></tbody></tgroup></table></tables>

SEQ ID 9294 (GBS663) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 137</figref> (lane 3; MW 89.5 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 137</figref> (lane 5-7; MW 64.5 kDa), in <figref idrefs="DRAWINGS">FIG. 179</figref> (lane 11; MW 65 kDa) and in <figref idrefs="DRAWINGS">FIG. 65</figref> (lane 2; MW 61 kDa). Purified GBS663-His is shown in <figref idrefs="DRAWINGS">FIG. 231</figref>, lane 34. Purified GBS324-His is shown in lane 6 of <figref idrefs="DRAWINGS">FIG. 210</figref>.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 93

A DNA sequence (GBSx0095) was identified in <i>S. agalactiae </i>&lt;SEQ ID 319&gt; which encodes the amino acid sequence &lt;SEQ ID 320&gt;. This protein is predicted to be transmembrane protein OppB (oppB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00339" num="00339"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.77</entry><entry>Transmembrane</entry><entry>293-309 (281-313)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.77</entry><entry>Transmembrane</entry><entry>  21-37 (14-46)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.32</entry><entry>Transmembrane</entry><entry>115-131 (105-132)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.88</entry><entry>Transmembrane</entry><entry>144-160 (140-166)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.03</entry><entry>Transmembrane</entry><entry>238-254 (237-255)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5310(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8491&gt; which encodes amino acid sequence &lt;SEQ ID 8492&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00340" num="00340"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF73091 GB: AF103793 transmembrane protein</entry><entry /></row><row><entry>OppB [<i>Listeria monocytogenes</i>]</entry></row><row><entry>Identities = 147/304 (48%), Positives = 221/304 (72%), Gaps = 1/304 (0%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>MIKYILKRVAILLVTLWVVITLSFFLMQILPGTPYNNP-KLTEEMIALLNKQYGLDKPVW</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>M+KY LKRV  +L+TL+++ +++F LM+ LPGTPY N  KL++E I + N++YGL+  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MVKYTLKRVLYMLITLFIIASVTFVLMKFLPGTPYRNQEKLSDEQIHMTNEKYGLNDSIP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>QQYLTYLWNVLHGDFGTSYQSVNQPVSRMISLRLGVSVHLGVQALVFGVLGGILVGAISA</entry><entry>131</entry></row><row><entry /><entry /><entry> QY  Y+  ++ GD G S+Q  N+PVS ++S  +G SV L ++A+ FGV+ GIL+G I+A</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VQYFNYMTGLVKGDLGVSFQLDNRPVSEILSALIGPSVQLALEAMAFGVIFGILLGVIAA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>RHKNDKVDGILSVIATLGISMPSFIIGILLLDYFGFKWNLLPLSGWGTFSQTILPSLALG</entry><entry>191</entry></row><row><entry /><entry /><entry> ++N   D   + IA LG S+PSF+   +L  + G K  + P++GWGTF+ TILP+ AL</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>MYQNRWPDYTSTFIAILGKSVPSFVFATVLQYWLGAKLQIFPVAGWGTFADTILPAFALA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>192</entry><entry>LPTLASVSRFFRSEMIETLNSDYVQLARSKGMTIRQVTRKHAYRNSMIPILTLIGPLAAG</entry><entry>251</entry></row><row><entry /><entry /><entry>+  LA+ +RF R+E+I+   SDYV LA++KG +  +V  KHA RN++IP++T++GPL+</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>MFPLATAARFMRTELIDVFASDYVLLAKAKGNSRTEVAVKHAIRNALIPLITVLGPLSVA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>252</entry><entry>LLTGSALIEQIFSIPGIGQQFVTSIPTKDYPVIMGTTIVYAVMLMVAILITDVVISIVDP</entry><entry>311</entry></row><row><entry /><entry /><entry>L+TGS +IE I+SIPGIG QFV+SI T DYPVIMGTTI++AVML+  IL+ D++  ++DP</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LMTGSLVIENIYSIPGIGSQFVSSIQTNDYPVIMGTTILFAVMLVFVILVVDILYGLIDP</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>312</entry><entry>RVRL</entry><entry>315</entry></row><row><entry /><entry /><entry>R+R+</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>RIRV</entry><entry>304</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 64.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 9069&gt; which encodes amino acid sequence &lt;SEQ ID 9070&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00341" num="00341"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="98pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.81</entry><entry>Transmembrane</entry><entry>466-482 (463-493)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.10</entry><entry>Transmembrane</entry><entry>419-435 (418-440)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.78</entry><entry>Transmembrane</entry><entry>328-344 (322-348)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.41</entry><entry>Transmembrane</entry><entry>366-382 (365-384)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.09</entry><entry>Transmembrane</entry><entry>290-306 (287-311)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.97</entry><entry>Transmembrane</entry><entry>  17-33 (13-36)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4524(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS sequences follows:

<tables id="TABLE-US-00342" num="00342"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Score = 117 bits (291), Expect = 3e−28</entry><entry /></row><row><entry>Identities = 61/208 (29%), Positives = 121/208 (57%), Gaps = 4/208 (1%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>291</entry><entry>IGFFGVMFSYIVGLPLGLFMARFKNTYFDSFSTATMTFMLALPSIAV-IYVVRFLGGMVG</entry><entry>349</entry><entry /></row><row><entry /><entry /><entry>+G   ++F  + G+ +G   AR KN   D   +   T  +++PS  + I ++ + G</entry><entry /></row><row><entry>Sbjct:</entry><entry>99</entry><entry>LGVQALVFGVLGGILVGAISARHKNDKVDGILSVIATLGISMPSFIIGILLLDYFGFKWN</entry><entry>158</entry></row><row><entry /></row><row><entry>Query:</entry><entry>350</entry><entry>LPDSFPMLGASDPKSYILPALILGILNIPTTVIWFRRYLVDLQASDWVRFARSKGLSESE</entry><entry>409</entry></row><row><entry /><entry /><entry>L    P+ G       ILP+L LG+  + +   +FR  +++   SD+V+ ARSKG++  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>159</entry><entry>L---LPLSGWGTFSQTILPSLALGLPTLASVSRFFRSEMIETLNSDYVQLARSKGMTIRQ</entry><entry>215</entry></row><row><entry /></row><row><entry>Query:</entry><entry>410</entry><entry>IYRGHLFKNAMVPIVSGVPASIILAIGGATLTETVFAFPGMGKMLIDSIKSANNSMIVGL</entry><entry>469</entry></row><row><entry /><entry /><entry>+ R H ++N+M+PI++ +       + G+ L E +F+ PG+G+  + SI + +  +I+G</entry><entry /></row><row><entry>Sbjct:</entry><entry>216</entry><entry>VTRKHAYRNSMIPILTLIGPLAAGLLTGSALIEQIFSIPGIGQQFVTSIPTKDYPVIMGT</entry><entry>275</entry></row><row><entry /></row><row><entry>Query:</entry><entry>470</entry><entry>TFIFTVLSIVSLLLGDIVMTLVDPRIKL</entry><entry>497</entry></row><row><entry /><entry /><entry>T ++ V+ +V++L+ D+V+++VDPR++L</entry><entry /></row><row><entry>Sbjct:</entry><entry>276</entry><entry>TIVYAVMLMVAILITDVVISIVDPRVRL</entry><entry>303</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 94

A DNA sequence (GBSx0096) was identified in <i>S. agalactiae </i>&lt;SEQ ID 321&gt; which encodes the amino acid sequence &lt;SEQ ID 322&gt;. This protein is predicted to be transmembrane protein OppC (oppC). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00343" num="00343"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="14pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.52</entry><entry>Transmembrane</entry><entry>311-327 (307-333)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.80</entry><entry>Transmembrane</entry><entry>  42-58 (40-65)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.43</entry><entry>Transmembrane</entry><entry>142-158 (131-165)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.73</entry><entry>Transmembrane</entry><entry>182-198 (179-214)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.50</entry><entry>Transmembrane</entry><entry>257-273 (257-276)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5607(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00344" num="00344"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF73092 GB: AF103793 transmembrane protein OppC</entry><entry /></row><row><entry>[<i>Listeria monocytogenes</i>]</entry></row><row><entry>Identities = 157/325 (48%), Positives = 219/325 (67%),</entry></row><row><entry>Gaps = 4/325 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>20</entry><entry>EKIEKPALSFMQDAWRRLKKNKLAVVSLYLLALLLTFSLASNLFVTQKDANGFDSKKVTT</entry><entry>79</entry><entry /></row><row><entry /><entry /><entry>EKI +P+L+F+QD+W R++KNK A+VSL +LAL++  ++               ++++T</entry><entry /></row><row><entry>Sbjct:</entry><entry>22</entry><entry>EKINRPSLTFLQDSWLRIRKNKAALVSLIVLALVIIMAIVGPYLSQNLGPEHNINRQITE</entry><entry>81</entry></row><row><entry /></row><row><entry>Query:</entry><entry>80</entry><entry>YRNLPPKLSS--NLPFWNGSIKYAGNTESTDAYKSQNVPEKVKYALGTDSLGRSVAKRII</entry><entry>137</entry></row><row><entry /><entry /><entry>  +LPPK+    N+PFWNG     G  E  D YK  N+ E   Y LG+D+LGR    RI</entry><entry /></row><row><entry>Sbjct:</entry><entry>82</entry><entry>NASLPPEVQGFENMPFWNGHQSIGG--EDVDIYKQNNIKEGTYYWLGSDTLGRDQFARIW</entry><entry>139</entry></row><row><entry /></row><row><entry>Query:</entry><entry>138</entry><entry>VGIRISLLVAIAATFIDLIIGVTYGLVSGFAGGRLDTLMQRIVEVISSIPNLVIVTMLGL</entry><entry>197</entry></row><row><entry /><entry /><entry> G R+SL++A+ A   DL+IGV YGL+SG+ GGR+D  MQR++EVI +IPNLV+V ++ L</entry><entry /></row><row><entry>Sbjct:</entry><entry>140</entry><entry>AGTRVSLIIAVVAALCDLVIGVAYGLISGYVGGRVDNFMQRVLEVIGAIPNLVVVILMML</entry><entry>199</entry></row><row><entry /></row><row><entry>Query:</entry><entry>198</entry><entry>VLGNGITAIIISIAFTGWTSMSRQVRNLTLSYREREFVLAARSLGESPIKIAFKHILPNI</entry><entry>257</entry></row><row><entry /><entry /><entry>+L  GI +III+IA T W +M+R VR   L  + +EFV+A+ +LGES  KI  KH++PNI</entry><entry /></row><row><entry>Sbjct:</entry><entry>200</entry><entry>ILEPGIVSIIIAIAMTSWITMARVVRGQVLKRKNQEFVMASMTLGESTPKILIKHLIPNI</entry><entry>259</entry></row><row><entry /></row><row><entry>Query:</entry><entry>258</entry><entry>SGIIIVQIMMTIPSAIMYEAVLSAINLGVKPPTASLGSLISDAQENLQYYPYQVILPALA</entry><entry>317</entry></row><row><entry /><entry /><entry>SGIII+ IM +IPSAI +EA LS I LG+  P ASLG L++D  + LQ  PY ++ P +</entry><entry /></row><row><entry>Sbjct:</entry><entry>260</entry><entry>SGIIIINIMFSIPSAIFFEAFLSFIGLGLPAPAASLGVLVNDGYKTLQVLPYMILYPCIV</entry><entry>319</entry></row><row><entry /></row><row><entry>Query:</entry><entry>318</entry><entry>LVMISLAFILLGDGLRDAFDPKSSD</entry><entry>342</entry></row><row><entry /><entry /><entry>L +I +AF L+ DGLRDAFDPK  D</entry><entry /></row><row><entry>Sbjct:</entry><entry>320</entry><entry>LCIIMIAFNLIADGLRDAFDPKMRD</entry><entry>344</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 323&gt; which encodes the amino acid sequence &lt;SEQ ID 324&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00345" num="00345"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="14pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.30</entry><entry>Transmembrane</entry><entry>  43-59 (37-65)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.49</entry><entry>Transmembrane</entry><entry>111-127 (109-135)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.26</entry><entry>Transmembrane</entry><entry>279-295 (270-298)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.88</entry><entry>Transmembrane</entry><entry>172-188 (172-188)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.61</entry><entry>Transmembrane</entry><entry>145-161 (145-165)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.49</entry><entry>Transmembrane</entry><entry>223-239 (223-239)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5118(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00346" num="00346"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 91/325 (28%), Positives = 156/325 (48%),</entry><entry /></row><row><entry>Gaps = 34/325 (10%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>16</entry><entry>SSTQEKIEKPALSFMQDAWRRLKKNKLAVVSLYLLALLLTFSLASNLFVTQKDANGFDSK</entry><entry>75</entry><entry /></row><row><entry /><entry /><entry>S   E I+ PA S+ +  +R+    K  V  L +L  +L  S    +F        +D</entry><entry /></row><row><entry>Sbjct:</entry><entry>16</entry><entry>SEASEVIDTPAYSYWKSVFRQFFSKKSTVFMLVILVTVLMMSFIYPMFAN------YDFN</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>76</entry><entry>KVTTYRNLPPKLSSNLPFWNGSIKYAGNTESTDAYKSQNVPEKVKYALGTDSLGRSVAKR</entry><entry>135</entry></row><row><entry /><entry /><entry> V+   +                           +  + +    +Y  GTD  G+S+</entry><entry /></row><row><entry>Sbjct:</entry><entry>70</entry><entry>DVSNIND---------------------------FSKRYIWPNAEYWFGTDKNGQSLFDG</entry><entry>102</entry></row><row><entry /></row><row><entry>Query:</entry><entry>136</entry><entry>IIVGIRISLLVAIAATFIDLIIGVTYGLVSGFAGGRLDTLMQRIVEVISSIPNLVIVTML</entry><entry>195</entry></row><row><entry /><entry /><entry>+  G R S+L+++ AT I++ IGV  G + G +    D +M  I  +IS+IP+++I+ +L</entry><entry /></row><row><entry>Sbjct:</entry><entry>103</entry><entry>VWYGARNSILISVIATLINITIGVVLGAIWGVSKA-FDKVMIEIYNIISNIPSMLIIIVL</entry><entry>161</entry></row><row><entry /></row><row><entry>Query:</entry><entry>196</entry><entry>GLVLGNGITAIIISIAFTGWTSMSRQVRNLTLSYREREFVLAARSLGESPIKIAFKHILP</entry><entry>255</entry></row><row><entry /><entry /><entry>   LG G   +I++   TGW  ++  +R   L YR+ E+ LA+++LG    KIA K++LP</entry><entry /></row><row><entry>Sbjct:</entry><entry>162</entry><entry>TYSLGAGFWNLILAFCITGWIGVAYSIRVQILRYRDLEYNLASQTLGTPMYKIAVKNLLP</entry><entry>221</entry></row><row><entry /></row><row><entry>Query:</entry><entry>256</entry><entry>NISGIIIVQIMMTIPSAIMYEAVLSAINLGVKPPTASLGSLISDAQENLQYYPYQVILPA</entry><entry>315</entry></row><row><entry /><entry /><entry> +  +I+  +   +P  +  EA LS   +G+   T SLG  I++   NL    Y   +P</entry><entry /></row><row><entry>Sbjct:</entry><entry>222</entry><entry>QLVSVIMTMLSQMLPVYVSSEAFLSFFGIGLPTTTPSLGRFIANYSSNLTTNAYLFWIPL</entry><entry>281</entry></row><row><entry /></row><row><entry>Query:</entry><entry>316</entry><entry>LALVMISLAFILLGDGLRDAFDPKS</entry><entry>340</entry></row><row><entry /><entry /><entry>+ L+++SL   ++G  L DA DP+S</entry><entry /></row><row><entry>Sbjct:</entry><entry>282</entry><entry>VTLILVSLPLYIVGQNLADASDPRS</entry><entry>306</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 95

A DNA sequence (GBSx0097) was identified in <i>S. agalactiae </i>&lt;SEQ ID 325&gt; which encodes the amino acid sequence &lt;SEQ ID 326&gt;. This protein is predicted to be ATPase OppD (oppD). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00347" num="00347"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="14pt" align="left" /><colspec colname="2" colwidth="56pt" align="left" /><colspec colname="3" colwidth="91pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.85</entry><entry>Transmembrane</entry><entry>164-180 (163-180)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1341(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00348" num="00348"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF73093 GB: AF103793 ATPase OppD [<i>Listeria monocytogenes</i>]</entry><entry /></row><row><entry>Identities = 230/342 (67%), Positives = 283/342 (82%), Gaps = 2/342 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>ETILSVNNLHVDFHTYAGEVKAIRDVNFELKKGETLAIVGESGSGKSVTTRTLIGLNAK-</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>E +L V +L++ FHTYAGEVKAIR VNF+L KGETLAIVGESGSGKSVTT++++ L  +</entry><entry /></row><row><entry>Sbjct:</entry><entry>2</entry><entry>EKLLEVKDLNISFHTYAGEVKAIRGVNFDLYKGETLAIVGESGSGKSVTTKSIMRLLPEG</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>NSEI-SGNVQFKGRNLVELSEEEWTKVRGNEISMIFQDPMTSLDPTMKIGMQIAEPMMIH</entry><entry>121</entry></row><row><entry /><entry /><entry>NSEI SG + F G ++ +  E++  K+RG +I+MIFQDPMTSL+PTM IG QI+EP++ H</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>NSEIKSGQILFNGMDIAKAHEKQMQKIRGKDIAMIFQDPMTSLNPTMTIGKQISEPLIKH</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>QKISKKDALKLALELMKDVGIPNAEEHINDYPHQWSGGMRQRAVIAIALAADPEILIADE</entry><entry>181</entry></row><row><entry /><entry /><entry>QKISK +A K AL L++ VGI NAEE I  YPHQ+SGGMRQR VIAI+LA +P+ILIADE</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>QKISKHEAHKTALRLLQLVGIANAEERIKQYPHQFSGGMRQRVVIAISLACNPQILIADE</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>PTTALDVTIQAQILNLMKKIQAERDSSIVFITHDLGVVAGMADRVAVMYAGKIVEFGTVD</entry><entry>241</entry></row><row><entry /><entry /><entry>PTTALDVTIQAQIL+LMK +Q + D+SI+FITHDLGVVA +ADRVAVMY GKIVE GTVD</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>PTTALDVTIQAQILDLMKDLQKKIDTSIIFITHDLGVVANVADRVAVMYGGKIVEIGTVD</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>EVFYNPQHPYTWGLLNSMPTTDTESGSLESIPGTPPDLLNPPKGDAFAARNEFALDIDHE</entry><entry>301</entry></row><row><entry /><entry /><entry>E+FYNPQHPYTWGL++SMPT DT+   L  IPGTPPDLL+PPKGDAFAARN++A+ ID E</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>EIFYNPQHPYTWGLISSMPTLDTDDEELFVIPGTPPDLLHPPKGDAFAARNKYAMQIDLE</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>EEPPYFKVSETHFAATWLLDERSPKVLPPLPIQKRWEKWNEI</entry><entry>343</entry></row><row><entry /><entry /><entry>EEPP FKVS+TH+AATWLL   +P+V PP  + +R E++ E+</entry><entry /></row><row><entry>Sbjct:</entry><entry>302</entry><entry>EEPPLFKVSDTHYAATWLLHPDAPEVTPPDAVLRRQEQFAEL</entry><entry>343</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 72.

SEQ ID 326 (GBS375) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 64</figref> (lane 9; MW 42 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 71</figref> (lane 3; MW 67 kDa).

GBS375-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 215</figref>, lane 10.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 96

A DNA sequence (GBSx0098) was identified in <i>S. agalactiae </i>&lt;SEQ ID 327&gt; which encodes the amino acid sequence &lt;SEQ ID 328&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00349" num="00349"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3060 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00350" num="00350"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAA62692 GB: M57689 sporulation protein [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 195/308 (63%), Positives = 245/308 (79%), Gaps = 4/308 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTENRKKLVEVKNVSLTFNKGKANEVRAIDNVSFDIYEGEVFGLVGESGSGKTTVGRSIL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M E  +KL+E+K++   F   +   V+A+D++SFDIY+GE  GLVGESG GK+T GRSI+</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNELTEKLLEIKHLKQHFVTPRGT-VKAVDDLSFDIYKGETLGLVGESGCGKSTTGRSII</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KLYDISDGEITFNGEVISHLKG-KALHSFRKDAQMIFQDPQASLNGRMKIRDIVAEGLDI</entry><entry>119</entry></row><row><entry /><entry /><entry>+LY+ +DGE+ FNGE +   K  K L  F +  QMIFQDP ASLN RM + DI+AEGLDI</entry><entry /></row><row><entry>Sbjct:</entry><entry>60</entry><entry>RLYEATDGEVLFNGENVHGRKSRKKLLEFNRKMQMIFQDPYASLNPRMTVADIIAEGLDI</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>HKLAKSKSDRDSKVQALLDLVGLNKDHLTRYPHEFSGGQRQRIGIARALAVEPKFIIADE</entry><entry>179</entry></row><row><entry /><entry /><entry>HKLAK+K +R  +V  LL+ VGLNK+H  RYPHEFSGGQRQRIGIARALAV+P+FIIADE</entry><entry /></row><row><entry>Sbjct:</entry><entry>120</entry><entry>HKLAKTKKERMQRVHELLETVGLNKEHANRYPHEFSGGQRQRIGIARALAVDPEFIIADE</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>PISALDVSIQAQVVNLMQKLQREQGLTYLFIAHDLSMVKYISDRIGVMHWGKLLEVGTSD</entry><entry>239</entry></row><row><entry /><entry /><entry>PISALDVSIQAQVVNLM++LQ+E+GLTYLFIAHDLSMVKYISDRIGVM++GKL+E+  +D</entry><entry /></row><row><entry>Sbjct:</entry><entry>180</entry><entry>PISALDVSIQAQVVNLMKELQKEKGLTYLFIAHDLSMVKYISDRIGVMYFGKLVELAPAD</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>DVYNNPIHPYTKSLLSAIPEPDPESERQRVHQPYNPAIEQ--DGQERQMHEITPGHFVLS</entry><entry>297</entry></row><row><entry /><entry /><entry>++Y NP+HPYTKSLLSAIP PDP+ ER RV Q Y+P++ Q  DG+  +  E+ PGHFV+</entry><entry /></row><row><entry>Sbjct:</entry><entry>240</entry><entry>ELYENPLHPYTKSLLSAIPLPDPDYERNRVRQKYDPSVHQLKDGETMEFREVKPGHFVMC</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>298</entry><entry>TPQEAEEY</entry><entry>305</entry></row><row><entry /><entry /><entry>T  E + +</entry><entry /></row><row><entry>Sbjct:</entry><entry>300</entry><entry>TEAEFKAF</entry><entry>307</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 329&gt; which encodes the amino acid sequence &lt;SEQ ID 330&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00351" num="00351"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3900(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00352" num="00352"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 164/306 (53%), Positives = 228/306 (73%), Gaps = 3/306 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>KKLVEVKNVSLTFNKGKANEVRAIDNVSFDIYEGEVFGLVGESGSGKTTVGRSILKLYDI</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>+KLVEVK++ ++F +GK   V A+ N +F I +GE F LVGESGSGKTT+GR+I+ L D</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>EKLVEVKDLEISFGEGKKKFV-AVKNANFFIKKGETFSLVGESGSGKTTIGRAIIGLNDT</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>SDGEITFNGEVISHLKGKA-LHSFRKDAQMIFQDPQASLNGRMKIRDIVAEGLDIHKLAK</entry><entry>124</entry></row><row><entry /><entry /><entry>S G+I ++G+VI+  K K+  +   +  QMIFQDP ASLN R  +  I++EGL    L K</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>SSGQILYDGKVINGRKSKSEANELIRKIQMIFQDPAASLNERATVDYIISEGLYNFNLFK</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>SKSDRDSKVQALLDLVGLNKDHLTRYPHEFSGGQRQRIGIARALAVEPKFIIADEPISAL</entry><entry>184</entry></row><row><entry /><entry /><entry>++ +R  K++ ++  VGL  +HLTRYPHEFSGGQRQRIGIARAL + P+F+IADEPISAL</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>TEEERKEKIKNMMAEVGLLSEHLTRYPHEFSGGQRQRIGIARALVMNPEFVIADEPISAL</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>DVSIQAQVVNLMQKLQREQGLTYLFIAHDLSMVKYISDRIGVMHWGKLLEVGTSDDVYNN</entry><entry>244</entry></row><row><entry /><entry /><entry>DVS++AQV+NL++++Q E+GLTYLFIAHDLS+V++ISDRI V+H G ++EV  +++++NN</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>DVSVRAQVLNLLKRMQAEKGLTYLFIAHDLSVVRFISDRIAVIHKGVIVEVAETEELFNN</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>PIHPYTKSLLSAIPEPDPESERQRVHQPYNPAIEQDGQER-QMHEITPGHFVLSTPQEAE</entry><entry>303</entry></row><row><entry /><entry /><entry>PIHPYT+SLLSA+P PDP  ERQ+    Y+P       ++  M EI P HFV +   E E</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>PIHPYTQSLLSAVPIPDPILERQKELVVYHPDQHDYTLDKPSMVEIKPNHFVWANQAEIE</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>304</entry><entry>EYKKQI</entry><entry>309</entry></row><row><entry /><entry /><entry>+Y+K++</entry></row><row><entry>Sbjct:</entry><entry>302</entry><entry>KYQKEL</entry><entry>307</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 97

A repeated DNA sequence (GBSx0099) was identified in <i>S. agalactiae </i>&lt;SEQ ID 331&gt; which encodes the amino acid sequence &lt;SEQ ID 332&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00353" num="00353"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3021(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 98

A repeated DNA sequence (GBSx0100) was identified in <i>S. agalactiae </i>&lt;SEQ ID 333&gt; which encodes the amino acid sequence &lt;SEQ ID 334&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00354" num="00354"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0352(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 99

A repeated DNA sequence (GBSx0101) was identified in <i>S. agalactiae </i>&lt;SEQ ID 335&gt; which encodes the amino acid sequence &lt;SEQ ID 336&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00355" num="00355"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5857(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 100

A repeated DNA sequence (GBSx0103) was identified in <i>S. agalactiae </i>&lt;SEQ ID 337&gt; which encodes the amino acid sequence &lt;SEQ ID 338&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00356" num="00356"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1472(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 101

A repeated DNA sequence (GBSx0104) was identified in <i>S. agalactiae </i>&lt;SEQ ID 339&gt; which encodes the amino acid sequence &lt;SEQ ID 340&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00357" num="00357"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0111(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 102

A repeated DNA sequence (GBSx0105) was identified in <i>S. agalactiae </i>&lt;SEQ ID 341&gt; which encodes the amino acid sequence &lt;SEQ ID 342&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00358" num="00358"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5628(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 103

A repeated DNA sequence (GBSx0106) was identified in <i>S. agalactiae </i>&lt;SEQ ID 343&gt; which encodes the amino acid sequence &lt;SEQ ID 344&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00359" num="00359"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2059(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database;

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 104

A repeated DNA sequence (GBSx0107) was identified in <i>S. agalactiae </i>&lt;SEQ ID 345&gt; which encodes the amino acid sequence &lt;SEQ ID 346&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00360" num="00360"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2045(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 105

A DNA sequence (GBSx0108) was identified in <i>S. agalactiae </i>&lt;SEQ ID 347&gt; which encodes the amino acid sequence &lt;SEQ ID 348&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00361" num="00361"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3031(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00362" num="00362"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11822 GB: Z99104 similar to hypothetical proteins [<i>Bacillus</i></entry><entry /></row><row><entry><i>subtilis</i>]</entry></row><row><entry>Identities = 125/282 (44%), Positives = 184/282 (64%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKIFEKAPAKLNLGLDIKGRCDDGYHELAMIMVSIDLNDYVTISELKEDCIVIDSDSSKM</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+I EKAPAK+NL LD+  +  DGYHE+ MIM +IDL D + ++EL ED + + S +  +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>PLNNDNDVFKAADIIKNQYGINKGVHIRLEKSIPVCAGLGGGSTDAAATIRALNRLWNLQ</entry><entry>120</entry></row><row><entry /><entry /><entry>P +  N  ++AA +IK++Y + KGV I + K IPV AGL GGS+DAAAT+R LNRLWNL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLN</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>MDYDEMVAIGFKIGSDVPYCLGGGCSLVLGKGEIVKPLPTLRPCWIVLVKPDFGISTKSI</entry><entry>180</entry></row><row><entry /><entry /><entry>+  + +  +G +IGSDV +C+ GG +L  G+GE +K + T   CW++L KP  G+ST  +</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEV</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>FRDIDCKSISRVDIDLLKSAILSSDYQLMVKSMGNSLEDITITKNPVISTIKERMLNSGA</entry><entry>240</entry></row><row><entry /><entry /><entry>+R +    I   D+  +  AI    +Q M   +GN LE +T+  +P ++ IK +M   GA</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>YRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>DVALMTGSGPTVFSMCSTEKKADRVFNSMKGFCKEVYKVRLL</entry><entry>282</entry></row><row><entry /><entry /><entry>D  LM+GSGPTVF +   E K  R++N ++GFC +VY VR++</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>DAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMI</entry><entry>282</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 349&gt; which encodes the amino acid sequence &lt;SEQ ID 350&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00363" num="00363"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.87</entry><entry>Transmembrane</entry><entry>28-44 (27-45)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2147(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00364" num="00364"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Identities = 33/52 (63%), Positives = 38/52 (72%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="224pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>126</entry><entry>MVAIGFKIGSDVPYCLGGGCSLVLGKGEIVKPLPTLRPCWIVLVKPDFGIST</entry><entry>177</entry><entry /></row><row><entry /><entry /><entry>M+ IG  IGSDVPYCL  GC+ V GKGE+V  +  L   W+VLVKPDFGIST</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MMDIGIPIGSDVPYCLLSGCAQVTGKGEVVCRILGLLSSWVVLVKPDFGIST</entry><entry>52</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 106

A DNA sequence (GBSx0109) was identified in <i>S. agalactiae </i>&lt;SEQ ID 351&gt; which encodes the amino acid sequence &lt;SEQ ID-352&gt;. This protein is predicted to be AdcR protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00365" num="00365"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1264(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00366" num="00366"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA96184 GB: Z71552 AdcR protein [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 77/146 (52%), Positives = 117/146 (79%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTVLEQKLDHLVSQILLKAENQHELLFGTCQSDVKLTNTQEHILMLLSQEQLTNSDLAKK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  L + ++  +++++L+AENQHE+L G C S+V LTNTQEHILMLLS+E LTNS+LA++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRQLAKDINAFLNEVILQAENQHEILIGHCTSEVALTNTQEHILMLLSEESLTNSELARR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LNISQAAVTKAVKSLISQDMLKANKDSKDARITYFELSELAKPIADEHTHHHDNTLGVYG</entry><entry>120</entry></row><row><entry /><entry /><entry>LN+SQAAVTKA+KSL+ + ML+ +KDSKDAR+ +++L++LA+PIA+EH HHH++TL  Y</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LNVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEHHHHHEHTLLTYE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>RLVNHFSKDEKVVLERFLDLFSRELE</entry><entry>146</entry></row><row><entry /><entry /><entry>++   F+ +E+ V++RFL     E++</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>QVATQFTPNEQKVIQRFLTALVGEIK</entry><entry>146</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 353&gt; which encodes the amino acid sequence &lt;SEQ ID 354&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00367" num="00367"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1536(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00368" num="00368"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 106/147 (72%), Positives = 126/147 (85%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTVLEQKLDHLVSQILLKAENQHELLFGTCQSDVKLTNTQEHILMLLSQEQLTNSDLAKK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M +LE+KLD+LV+ ILLKAENQHELLFG CQSDVKLTNTQEHILMLLSQ++LTN+DLAK</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MGILEKKLDNLVNTILLKAENQHELLFGACQSDVKLTNTQEHILMLLSQQRLTNTDLAKA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LNISQAAVTKAVKSLISQDMLKANKDSKDARITYFELSELAKPIADEHTHHHDNTLGVYG</entry><entry>120</entry></row><row><entry /><entry /><entry>LNISQAAVTKA+KSL+ QDML   KD+ DAR+TYFEL+ELAKPIA EHTHHHD TL VY</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LNISQAAVTKAIKSLVKQDMLAGTKDTVDARVTYFELTELAKPIASEHTHHHDETLNVYN</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>RLVNHFSKDEKVVLERFLDLFSRELEG</entry><entry>147</entry></row><row><entry /><entry /><entry>RL+  FS  E  ++++F+ +F+ ELEG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>RLLQKFSAKELEIVDKFVTVFAEELEG</entry><entry>147</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 107

A DNA sequence (GBSx0110) was identified in <i>S. agalactiae </i>&lt;SEQ ID 355&gt; which encodes the amino acid sequence &lt;SEQ ID 356&gt;. This protein is predicted to be AdcC protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00369" num="00369"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1089(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00370" num="00370"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA96186 GB: Z71552 AdcC protein [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 182/231 (78%), Positives = 206/231 (88%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MRYITVSGLTFQYDSDPVLEGVNYHLDSGEFVTLTGENGAAKSTLIKATLGILTPKVGTV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MRYITV  L+F YD +PVLE +NY +DSGEFVTLTGENGAAK+TLIKA+LGIL P++G V</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRYITVEDLSFYYDKEPVLEHINYCVDSGEFVTLTGENGAAKTTLIKASLGILQPRIGKV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NISKENKEGKKLRIAYLPQQIASFNAGFPSSVYEFVKSGRYPRNGWFRRLTKHDEEHIRV</entry><entry>120</entry></row><row><entry /><entry /><entry> ISK N +GKKLRIAYLPQQIASFNAGFPS+VYEFVKSGRYPR GWFRRL  HDEEHI+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>AISKTNTQGKKLRIAYLPQQIASFNAGFPSTVYEFVKSGRYPRKGWFRRLNAHDEEHIKA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>SLEAVGMWDNRHKKIGSLSGGQKQRAVIARMFASDPDIFVLDEPTTGMDAGTTEKFYELM</entry><entry>180</entry></row><row><entry /><entry /><entry>SL++VGMW++R K++GSLSGGQKQRAVIARMFASDPD+F+LDEPTTGMDAG+  +FYELM</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SLDSVGMWEHRDKRLGSLSGGQKQRAVIARMFASDPDVFILDEPTTGMDAGSKNEFYELM</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>HHNAHKHGKSVLMITHDPDEVKGYADRNIHLVRNQSLPWRCFNVHTNEMEV</entry><entry>231</entry></row><row><entry /><entry /><entry>HH+AH HGK+VLMITHDP+EVK YADRNIHLVRNQ  PWRCFNVH N  EV</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>HHSAHHHGKAVLMITHDPEEVKDYADRNIHLVRNQDSPWRCFNVHENGQEV</entry><entry>231</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 357&gt; which encodes the amino acid sequence &lt;SEQ ID 358&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00371" num="00371"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible Site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2722(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00372" num="00372"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 190/232 (81%), Positives = 214/232 (91%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MRYITVSGLTFQYDSDPVLEGVNYHLDSGEFVTLTGENGAAKSTLIKATLGILTPKVGTV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MRYI+V  L+FQY+S+PVLEG+ YHLDSGEFVT+TGENGAAKSTLIKATLGIL PK G V</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRYISVKNLSFQYESEPVLEGITYHLDSGEFVTMTGENGAAKSTLIKATLGILQPKAGRV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>NISKENKEGKKLRIAYLPQQIASFNAGFPSSVYEFVKSGRYPRNGWFRRLTKHDEEHIRV</entry><entry>120</entry></row><row><entry /><entry /><entry> I+K+NK+GK+LRIAYLPQQ+ASFNAGFPS+VYEFVKSGRYPR+GWFR L KHDEEH++</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TIAKKNKDGKQLRIAYLPQQVASFNAGFPSTVYEFVKSGRYPRSGWFRHLNKHDEEHVQA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>SLEAVGMWDNRHKKIGSLSGGQKQRAVIARMFASDPDIFVLDEPTTGMDAGTTEKFYELM</entry><entry>180</entry></row><row><entry /><entry /><entry>SLEAVGMW+NRHK+IGSLSGGQKQR VIARMFASDPDIFVLDEPTTGMD+GTT+ FYELM</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SLEAVGMWENRHKRIGSLSGGQKQRVVIARMFASDPDIFVLDEPTTGMDSGTTDTFYELM</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>HHNAHKHGKSVLMITHDPDEVKGYADRNIHLVRNQSLPWRCFNVHTNEMEVE</entry><entry>232</entry></row><row><entry /><entry /><entry>HH+AH+HGKSVLMITHDP+EVK YADRNIHLVRNQ LPWRCFN+H  E + E</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>HHSAHQHGKSVLMITHDPEEVKAYADRNIHLVRNQKLPWRCFNIHEAETDDE</entry><entry>232</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 108

A DNA sequence (GBSx0111) was identified in <i>S. agalactiae </i>&lt;SEQ ID 359&gt; which encodes the amino acid sequence &lt;SEQ ID 360&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00373" num="00373"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2299(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 109

A DNA sequence (GBSx0112) was identified in <i>S. agalactiae </i>&lt;SEQ ID 361&gt; which encodes the amino acid sequence &lt;SEQ ID 362&gt;. This protein is predicted to be AdcB protein (znuB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00374" num="00374"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −14.33</entry><entry>Transmembrane</entry><entry>145-161 (136-172)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.57</entry><entry>Transmembrane</entry><entry>  29-45 (20-47)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.56</entry><entry>Transmembrane</entry><entry>261-277 (255-280)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.70</entry><entry>Transmembrane</entry><entry>231-247 (227-253)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.63</entry><entry>Transmembrane</entry><entry>101-117 (99-121)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.94</entry><entry>Transmembrane</entry><entry>186-202 (183-225)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.82</entry><entry>Transmembrane</entry><entry>  55-71 (54-74)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.61</entry><entry>Transmembrane</entry><entry>206-222 (203-225)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.03</entry><entry>Transmembrane</entry><entry>  78-94 (75-94)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6731(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9487&gt; which encodes amino acid sequence &lt;SEQ ID 9488&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00375" num="00375"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA96187 GB: Z71552 AdcB protein [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 197/263 (74%), Positives = 236/263 (88%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>LLDMLSYDFMQRALLAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGIS</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>+L +LSYDF+QRA LAV+A+S+F+P+LG FLILRRQSLMSDTLSHVSL+GVA G+VLGIS</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLSLLSYDFIQRAFLAVIAMSLFSPVLGTFLILRRQSLMSDTLSHVSLSGVAFGLVLGIS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>PTWSTIFVVTLAAVVLEYLRTVYKHYMEISTAILMSMGLAISLIVMSKAHNVGNVSLEQY</entry><entry>132</entry></row><row><entry /><entry /><entry>PT STI +V +AAV LEYLRTVYK +MEI TAILMS GLA+SLIVMSK  +  ++SL+QY</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PTVSTIAIVLIAAVFLEYLRTVYKSFMEIGTAILMSTGLAVSLIVMSKGKSSSSMSLDQY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>133</entry><entry>LFGSIITIGKEQVIALFVIALITFILTILFIRPMYILTFDEDTAFVDGLPVRTMSILFNV</entry><entry>192</entry></row><row><entry /><entry /><entry>LFGSI+TI +EQVI+LFVIA +  ILT LF+RPMYILTFDEDTAFVDGLPVRTMSILFN+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LFGSIVTISEEQVISLFVIAAVVLILTFLFLRPMYILTFDEDTAFVDGLPVRTMSILFNM</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>193</entry><entry>VTGIAIALTIPAAGALLVSTIMVLPASIAMRLGRNFKTVIFLGMLIGFVGMVAGIFLSYY</entry><entry>252</entry></row><row><entry /><entry /><entry>VTG+AIAL IPAAGALLVSTIMVLPASIA+RLG+NFK+V+ L   IGF+GMVAG+++SYY</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VTGVAIALMIPAAGALLVSTIMVLPASIALRLGKNFKSVMLLASAIGFLGMVAGLYISYY</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>253</entry><entry>WETPASATITMIFIGIFLLVSLV</entry><entry>275</entry></row><row><entry /><entry /><entry> ETPASA+IT+IF+ +F+L+SLV</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AETPASASITIIFVTVFILISLV</entry><entry>263</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 363&gt; which encodes the amino acid sequence &lt;SEQ ID 364&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00376" num="00376"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −14.97</entry><entry>Transmembrane</entry><entry>135-151 (123-162)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.08</entry><entry>Transmembrane</entry><entry>  68-84 (44-86)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.95</entry><entry>Transmembrane</entry><entry>  20-36 (19-37)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.90</entry><entry>Transmembrane</entry><entry>251-267 (245-270)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.58</entry><entry>Transmembrane</entry><entry>221-237 (217-243)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.42</entry><entry>Transmembrane</entry><entry> 91-107 (89-111)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.78</entry><entry>Transmembrane</entry><entry>176-192 (171-215)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.82</entry><entry>Transmembrane</entry><entry>  45-61 (44-67)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.61</entry><entry>Transmembrane</entry><entry>196-212 (193-215)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6986(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00377" num="00377"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA96187 GB: Z71552 AdcB protein [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 195/262 (74%), Positives = 239/262 (90%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MLDILFYDFMQRAVMAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGIS</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>ML +L YDF+QRA +AV+A+S+F+P+LG FLILRRQSLMSDTLSHVSL+GVA G+VLGIS</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLSLLSYDFIQRAFLAVIAMSLFSPVLGTFLILRRQSLMSDTLSHVSLSGVAFGLVLGIS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>PTITTIIVVVLAAILLEYLRVVYKHYMEISTAILMSLGLALSLIIMSKSHSSSSMSLEQY</entry><entry>122</entry></row><row><entry /><entry /><entry>PT++TI +V++AA+ LEYLR VYK +MEI TAILMS GLA+SLI+MSK  SSSSMSL+QY</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PTVSTIAIVLIAAVFLEYLRTVYKSFMEIGTAILMSTGLAVSLIVMSKGKSSSSMSLDQY</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>LFGSIITISMEQVVALFAIAAIILILTVLFIRPMYILTFDEDTAFVDGLPVRLMSVLFNI</entry><entry>182</entry></row><row><entry /><entry /><entry>LFGSI+TIS EQV++LF IAA++LILT LF+RPMYILTFDEDTAFVDGLPVR MS+LFN+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LFGSIVTISEEQVISLFVIAAVVLILTFLFLRPMYILTFDEDTAFVDGLPVRTMSILFNM</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>VTGVAIALTIPAAGALLVSTIMVLPASIAMRLGKNFKTVILLGIVIGFSGMLSGIFLSYF</entry><entry>242</entry></row><row><entry /><entry /><entry>VTGVAIAL IPAAGALLVSTIMVLPASIA+RLGKNFK+V+LL   IGF GM++G+++SY+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VTGVAIALMIPAAGALLVSTIMVLPASIALRLGKNFKSVMLLASAIGFLGMVAGLYISYY</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>FETPASATITMIFISIFLLVSL</entry><entry>264</entry></row><row><entry /><entry /><entry> ETPASA+IT+IF+++F+L+SL</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AETPASASITIIFVTVFILISL</entry><entry>262</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00378" num="00378"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 223/270 (82%), Positives = 252/270 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>12</entry><entry>MLLDMLSYDFMQRALLAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>++LD+L YDFMQRA++AVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>VMLDILFYDFMQRAVMAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>SPTWSTIFVVTLAAVVLEYLRTVYKHYMEISTAILMSMGLAISLIVMSKAHNVGNVSLEQ</entry><entry>131</entry></row><row><entry /><entry /><entry>SPT +TI VV LAA++LEYLR VYKHYMEISTAILMS+GLA+SLI+MSK+H+  ++SLEQ</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>SPTITTIIVVVLAAILLEYLRVVYKHYMEISTAILMSLGLALSLIIMSKSHSSSSMSLEQ</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>YLFGSIITIGKEQVIALFVIALITFILTILFIRPMYILTFDEDTAFVDGLPVRTMSILFN</entry><entry>191</entry></row><row><entry /><entry /><entry>YLFGSIITI  EQV+ALF IA I  ILT+LFIRPMYILTFDEDTAFVDGLPVR MS+LFN</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>YLFGSIITISMEQVVALFAIAAIILILTVLFIRPMYILTFDEDTAFVDGLPVRLMSVLFN</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>192</entry><entry>VVTGIAIALTIPAAGALLVSTIMVLPASIAMRLGRNFKTVIFLGMLIGFVGMVAGIFLSY</entry><entry>251</entry></row><row><entry /><entry /><entry>+VTG+AIALTIPAAGALLVSTIMVLPASIAMRLG+NFKTVI LG++IGF GM++GIFLSY</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>IVTGVAIALTIPAAGALLVSTIMVLPASIAMRLGKNFKTVILLGIVIGFSGMLSGIFLSY</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>252</entry><entry>YWETPASATITMIFIGIFLLVSLVGLLRKR</entry><entry>281</entry></row><row><entry /><entry /><entry>++ETPASATITMIFI IFLLVSL G+L+KR</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>FFETPASATITMIFISIFLLVSLGGMLKKR</entry><entry>271</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 110

A DNA sequence (GBSx0113) was identified in <i>S. agalactiae </i>&lt;SEQ ID 365&gt; which encodes the amino acid sequence &lt;SEQ ID 366&gt;. This protein is predicted to be streptodornase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00379" num="00379"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2601(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00380" num="00380"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA59264 GB: X84793 streptodornase [<i>Streptococcus pyogenes</i>]</entry><entry /></row><row><entry>Identities = 58/167 (34%), Positives = 85/167 (50%),</entry></row><row><entry>Gaps = 30/167 (17%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>TPIYEGNNLVPSRVELQYVGIDKQGKLLEIKLGGGKEQVDEYGVTTVTLENTSPLAKIDY</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>TP+Y+G+ L+P  V +  +  D                +DE    TV + N      IDY</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>TPVYQGSELLPRAVLVSALSSDGF--------------IDE----TVRVFNNVAGFNIDY</entry><entry>286</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>KTGMLIKEDGKQAEEGEDPNSDADENEAAIE-SASDIEENTNTNTSESDTNNVAPQNRIV</entry><entry>120</entry></row><row><entry /><entry /><entry>+ G L+ E          P ++ D  E  +E +   IE+  +T+T + D  N++ Q + V</entry></row><row><entry>Sbjct:</entry><entry>287</entry><entry>QNGGLLTES---------PVTETDNVEENVEDNIETIEDEVDTDTLKKDDENISLQ-KTV</entry><entry>336</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>YVANKGRSNTYWYSLENI-KNANTANIVQMTEQEALNQHKHHSTTEA</entry><entry>166</entry></row><row><entry /><entry /><entry>YVA+ G SN YWYS EN+ KN N   +V+M+EQ AL + KHHS  EA</entry></row><row><entry>Sbjct:</entry><entry>337</entry><entry>YVASSGLSNVYWYSKENMPKNVNLDKVVEMSEQTALARGKHHSAQEA</entry><entry>383</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 367&gt; which encodes the amino acid sequence &lt;SEQ ID 368&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00381" num="00381"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00382" num="00382"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 51/90 (56%), Positives = 66/90 (72%), Gaps = 4/90 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTPIYEGNNLVPSRVELQYVGIDKQGKLLEIKLGGGKEQVDEYGVTTVTLENTSPLAKID</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+TP+Y  N LVP +V LQYVGID+ G LL+IKLG  KE VD +GVT+VTL+N SPLA++D</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>VTPVYHKNELVPRQVVLQYVGIDENGDLLQIKLGSEKESVDNFGVTSVTLDNVSPLAELD</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YKTGMLIKEDGKQAEEGEDPNSDADENEAA</entry><entry>90</entry></row><row><entry /><entry /><entry>Y+TGM++  D  Q E  ED N + +E E A</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>YQTGMML--DSTQNE--EDSNLETEEFEEA</entry><entry>267</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 111

A DNA sequence (GBSx0114) was identified in <i>S. agalactiae </i>&lt;SEQ ID 369&gt; which encodes the amino acid sequence &lt;SEQ ID 370&gt;. This protein is predicted to be tyrosyl-tRNA synthetase (tyrS-1). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00383" num="00383"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 60</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3618(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00384" num="00384"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC00303 GB: AF008220 tyrosine tRNA synthetase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 234/420 (55%), Positives = 311/420 (73%), Gaps = 2/420 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>NIFDELKERGLVFQTTDEDALRKALEEGSVSYYTGYDPTADSLHLGHLVAILTSRRLQLA</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>N+ ++L  RGL+ Q TDE+ L K L E  +  Y+G+DPTADSLH+GHL+ ILT RR QLA</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>NLLEDLSFRGLIQQMTDEEGLNKQLNEEKIRLYSGFDPTADSLHIGHLLPILTLRRFQLA</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>GHKPYALVGGATGLIGDPSFKDVERSLQTKKTVVSWGNKIRGQLSNFLEFETGDNKAVLV</entry><entry>121</entry></row><row><entry /><entry /><entry>GH P ALVGGATGLIGDPS K  ER+L T   V  W  KI+ QLS FL+FE  +N AV+</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>GHHPIALVGGATGLIGDPSGKKAERTLNTADIVSEWSQKIKNQLSRFLDFEAAENPAVIA</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>NNYDWFSNISFIDFLRDVGKYFTVNYMMSKESVKKRIETGISYTEFAYQIMQGYDFYELN</entry><entry>181</entry></row><row><entry /><entry /><entry>NN+DW   ++ IDFLRDVGK F +NYM++K++V  RIE+GISYTEF+Y I+Q YDF  L</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>NNFDWIGKMNVIDFLRDVGKNFGINYMLAKDTVSSRIESGISYTEFSYMILQSYDFLNLY</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>KNYNVTLQIGGSDQWGNMTAGTELIRR--KSNGVSHVMTVPLITDSTGKKFGKSEGNAVW</entry><entry>239</entry></row><row><entry /><entry /><entry>++ N  LQIGGSDQWGN+TAG ELIR+  +    +  +T+PL+T + G KFGK+EG A+W</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>RDKNCKLQIGGSDQWGNITAGLELIRKSEEEGAKAFGLTIPLVTKADGTKFGKTEGGAIW</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>LDADKTSPYEMYQFWLNVMDADAVRFLKIFTFLSLKEIEDIRIQFEEAPHQRLAQKTLAR</entry><entry>299</entry></row><row><entry /><entry /><entry>LD +KTSPYE YQFW+N  D D V++LK FTFLS +EIE    + E AP +R AQK LA</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>LDKEKTSPYEFYQFWINTDDRDVVKYLKYFTFLSKEEIEAYAEKTETAPEKREAQKRLAE</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>EVVTLVHGEKAYKEAVNITEQLFAGNIKGLSVKELKQGLRGVPNYHVQTEDNLNIIDLLV</entry><entry>359</entry></row><row><entry /><entry /><entry>EV +LVHG +A ++A+NI++ LF+GNIK LS +++K G + VP+  V +   L+++D+LV</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>EVTSLVHGREALEQAINISQALFSGNIKELSAQDVKVGFKDVPSMEVDSTQELSLVDVLV</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>TSGVVNSKRQAREDVSNGAIYINGDRIQDLEYTISENDKLENEITVIRRGKKKYFVLNFK</entry><entry>419</entry></row><row><entry /><entry /><entry> S +  SKRQARED+ NGA+YING+R  ++ YT+S  D++EN+ TV+RRGKKKYF++ +K</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>QSKLSPSKRQAREDIQNGAVYINGERQTEINYTLSGEDRIENQFTVLRRGKKKYFLVTYK</entry><entry>422</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 371&gt; which encodes the amino acid sequence &lt;SEQ ID 372&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00385" num="00385"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2340(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00386" num="00386"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 344/418 (82%), Positives = 377/418 (89%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNIFDELKERGLVFQTTDEDALRKALEEGSVSYYTGYDPTADSLHLGHLVAILTSRRLQL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MNIF+ELK RGLVFQTTDE AL KAL EG VSYYTGYDPTADSLHLGHLVAILTSRRLQL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNIFEELKARGLVFQTTDEQALVKALTEGQVSYYTGYDPTADSLHLGHLVAILTSRRLQL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>AGHKPYALVGGATGLIGDPSFKDVERSLQTKKTVVSWGNKIRGQLSNFLEFETGDNKAVL</entry><entry>120</entry></row><row><entry /><entry /><entry>AGHKPYALVGGATGLIGDPSFKD ERSLQTK+TV+ W +KI+GQLS FL+FE GDNKA L</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>AGHKPYALVGGATGLIGDPSFKDAERSLQTKETVLEWSDKIKGQLSTFLDFENGDNKAEL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>VNNYDWFSNISFIDFLRDVGKYFTVNYMMSKESVKKRIETGISYTEFAYQIMQGYDFYEL</entry><entry>180</entry></row><row><entry /><entry /><entry>VNNYDWFS ISFIDFLRDVGKYFTVNYMNSK+SVKKRIETGISYTEFAYQIMQGYDFYEL</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VNNYDWFSQISFIDFLRDVGKYFTVNYMMSKDSVKKRIETGISYTEFAYQIMQGYDFYEL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>NKNYNVTLQIGGSDQWGNMTAGTELIRRKSNGVSHVMTVPLITDSTGKKFGKSEGNAVWL</entry><entry>240</entry></row><row><entry /><entry /><entry>N  +NVTLQIGGSDQWGNMTAGTEL+R+K++   HVMTVPLITDSTGKKFGKSEGNAVWL</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>NDKHNVTLQIGGSDQWGNMTAGTELLRKKADKTGHVMTVPLITDSTGKKFGKSEGNAVWL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>DADKTSPYEMYQEWLNVMDADAVRFLKIFTFLSLKEIEDIRIQFEEAPHQRLAQKTLARE</entry><entry>300</entry></row><row><entry /><entry /><entry>DADKTSPYEMYQFWLNVMD DAVRFLKIFTFLSL EI +I  QF  A H+RLAQKTLARE</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>DADKTSPYEMYQFWLNVMDDDAVRFLKIFTFLSLDEIAEIETQFNAARHERLAQKTLARE</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>VVTLVHGEKAYKEAVNITEQLFAGNIKGLSVKELKQGLRGVPNYHVQTEDNLNIIDLLVT</entry><entry>360</entry></row><row><entry /><entry /><entry>VVTLVHGE+AYK+A+NITEQLFAGNIK LS  ELKQGL  VPNYHVQ+ DN NI+++LV</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>VVTLVHGEEAYKQALNITEQLFAGNIKNLSANELKQGLSNVPNYHVQSIDNHNIVEILVA</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>SGVVNSKRQAREDVSNGAIYINGDRIQDLEYTISENDKLENEITVIRRGKKKYFVLNF</entry><entry>418</entry></row><row><entry /><entry /><entry>+ +  SKRQAREDV NGAIYINGDR+QDL+Y +S +DK+++++TVIRRGKKKY VL +</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>AKISPSKRQAREDVQNGAIYINGDRVQDLDYQLSNDDKIDDQLTVIRRGKKKYAVLTY</entry><entry>418</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 112

A DNA sequence (GBSx0115) was identified in <i>S. agalactiae </i>&lt;SEQ ID 373&gt; which encodes the amino acid sequence &lt;SEQ ID 374&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00387" num="00387"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.21</entry><entry>Transmembrane</entry><entry>36-52 (23-59)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5883(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00388" num="00388"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF04736 GB: AF101781 penicillin-binding protein 1b</entry><entry /></row><row><entry>[<i>Streptococcus pneumoniae</i>]</entry></row><row><entry>Identities = 445/769 (57%), Positives = 581/769 (74%), Gaps = 9/769 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KGNKKLNSSKLGDYTP----LEFGSIFLRI---VKLLSDFIYVIILLFVMLGVGLAVGYL</entry><entry>55</entry><entry /></row><row><entry /><entry /><entry>K  K     K G  T     L+  +IF  I   +K L + ++V+  L  MLG G+A+GY</entry></row><row><entry>Sbjct:</entry><entry>21</entry><entry>KNKKSARPGKKGSSTKKSKTLDKSAIFPAILLSIKALFNLLFVLGFLGGMLGAGIALGYG</entry><entry>80</entry></row><row><entry /></row><row><entry>Query:</entry><entry>56</entry><entry>ASQVDSVKVPSKNSLVTQVNTLTRVSRLTYSDKSQISEIATDLQRTPVAKDAISDNIKKA</entry><entry>115</entry></row><row><entry /><entry /><entry> +  D V+VP    LV QV  ++ +S +TYSD + I+ I +DL RT ++ + IS+N+KKA</entry></row><row><entry>Sbjct:</entry><entry>81</entry><entry>VALFDKVRVPQTEELVNQVKDISSISEITYSDGTVIASIESDLLRTSISSEQISENLKKA</entry><entry>140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>116</entry><entry>IIATEDENFNDHKGVVPKAVLRAAAGSVLGFGESSGGSTLTQQLLKQQILGDDPSFKRKS</entry><entry>175</entry></row><row><entry /><entry /><entry>IIATEDE+F +HKGVVPKAV+RA  G  +G G SSGGSTLTQQL+KQQ++GD P+  RK+</entry></row><row><entry>Sbjct:</entry><entry>141</entry><entry>IIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKA</entry><entry>200</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>KEIIYALALERYMDKDSILSDYLNVSPFGRNNKGQNIAGIEEAAQGIFGVSAKDLTIPQA</entry><entry>235</entry></row><row><entry /><entry /><entry> EI+ ALALER M+KD IL+ YLNV+PFGRNNKGQNIAG  +AA+GIFGV A  LT+PQA</entry></row><row><entry>Sbjct:</entry><entry>201</entry><entry>AEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQA</entry><entry>260</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>AFLAGLPQSPIVYSPYTADAQLKSDKDLSFGIKRQKNVLYNMYRTRALTKDEYKSYKDYD</entry><entry>295</entry></row><row><entry /><entry /><entry>AFLAGLPQSPI YSPY    +LKSD+DL  G++R K VLY+MYRT AL+KDEY  YKDYD</entry></row><row><entry>Sbjct:</entry><entry>261</entry><entry>AFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYD</entry><entry>320</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>IKKDFIKPAVATTNHHDYLYYSALSEAQKVMYNYLIKKDNVSEHDLKNDETRATYRHRAI</entry><entry>355</entry></row><row><entry /><entry /><entry>+K+DF+     T    DYLY++ L+EAQ+ MY+YL ++DNVS  +LKN+ T+  YR  A</entry></row><row><entry>Sbjct:</entry><entry>321</entry><entry>LKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAA</entry><entry>380</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>EEIQQGGYTIKTTINKSVYQAMQDAAAQYGGLLDDGTGKVQMGNVLTDNSSGAIIGFIGG</entry><entry>415</entry></row><row><entry /><entry /><entry>+EI+ GGY I TTI++ ++ AMQ A A YG LLDDGTG+V++GNVL DN +GAI+GF+GG</entry></row><row><entry>Sbjct:</entry><entry>381</entry><entry>KEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGG</entry><entry>440</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>RNYSENQNNHAFDTARSPGSSIKPILPYGIAIDQGMLGSGSVLSNYPTTYSSGEKIMHAD</entry><entry>475</entry></row><row><entry /><entry /><entry>RNY ENQNNHAFDT RSP S+ KP+L YGIAIDQG++GS ++LSNYPT +++G  IM+A+</entry></row><row><entry>Sbjct:</entry><entry>441</entry><entry>RNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYAN</entry><entry>500</entry></row><row><entry /></row><row><entry>Query:</entry><entry>476</entry><entry>EEGTAMVNLQESLDISWNIPAFWTYKMLRDRGVDVKNYMEKLDYPIENFGIESLPLGGGI</entry><entry>535</entry></row><row><entry /><entry /><entry> +GT M+ L E+L+ SWNIPA+WTY+MLR+ GVDVK YMEK+ Y I  +GIESLP+GGGI</entry></row><row><entry>Sbjct:</entry><entry>501</entry><entry>SKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGI</entry><entry>560</entry></row><row><entry /></row><row><entry>Query:</entry><entry>536</entry><entry>DTSVAQQTNLYQMIANGGVYHKQYMIESIEDSNGKVIYNHESKPVRVFSKATATILQQLL</entry><entry>595</entry></row><row><entry /><entry /><entry>+ +VAQ TN YQ +AN GVYH++++I  IE ++G+V+Y ++ KPV+V+SKATATI+Q LL</entry></row><row><entry>Sbjct:</entry><entry>561</entry><entry>EVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLL</entry><entry>620</entry></row><row><entry /></row><row><entry>Query:</entry><entry>596</entry><entry>HGPINSGKTTTFKNRLQGLNSGLAGVDWIGKTGTTNSTSDVWLMLSTPKVTLGGWAGHDN</entry><entry>655</entry></row><row><entry /><entry /><entry>   ++S  TTTFK+ L  LN  LA  DWIGKTGTTN   ++WLMLSTP++TLGGW GHD+</entry></row><row><entry>Sbjct:</entry><entry>621</entry><entry>REVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDD</entry><entry>680</entry></row><row><entry /></row><row><entry>Query:</entry><entry>656</entry><entry>NASLAKLTGYNNNANYMAHLVNAINNADGNTFGKSERFRLDDSVIKAKVLKSTGLQPGVV</entry><entry>715</entry></row><row><entry /><entry /><entry>N SL++  GY+NN+NYMAHLVNAI  A  + +G +ERF LD SV+K++VLKSTG +PG V</entry></row><row><entry>Sbjct:</entry><entry>681</entry><entry>NHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWG-NERFALDPSVVKSEVLKSTGQKPGKV</entry><entry>739</entry></row><row><entry /></row><row><entry>Query:</entry><entry>716</entry><entry>TVNGRRITVGGESTTSYWA-KNGPGTMTYRFAIGGTDSDYQKAWSTLGG</entry><entry>763</entry></row><row><entry /><entry /><entry>+V G+ + V G + TSYWA K+G    +YRFAIGG+D+DYQ AWS++ G</entry></row><row><entry>Sbjct:</entry><entry>740</entry><entry>SVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVG</entry><entry>788</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 375&gt; which encodes the amino acid sequence &lt;SEQ ID 376&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00389" num="00389"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.83</entry><entry>Transmembrane</entry><entry>39-55 (32-60)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2932(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00390" num="00390"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF04736 GB: AF101781 penicillin-binding protein 1b</entry><entry /></row><row><entry>[<i>Streptococcus pneumoniae</i>]</entry></row><row><entry>Identities = 438/739 (59%), Positives = 580/739 (78%), Gaps = 2/739 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>27</entry><entry>PVLLRTLRLLSNFFYIVIFLFGMMGFGMAFGYLASQIESVKVPSKESLVKQVESLTMISQ</entry><entry>86</entry><entry /></row><row><entry /><entry /><entry>P +L +++ L N  +++ FL GM+G G+A GY  +  + V+VP  E LV QV+ ++ IS+</entry></row><row><entry>Sbjct:</entry><entry>48</entry><entry>PAILLSIKALFNLLFVLGFLGGMLGAGIALGYGVALFDKVRVPQTEELVNQVKDISSISE</entry><entry>107</entry></row><row><entry /></row><row><entry>Query:</entry><entry>87</entry><entry>MNYSDNSLISTLDTDLLRTPVANDAISENIKKAIVSTEDEHFQEHKGIVPKAVFRATLAS</entry><entry>146</entry></row><row><entry /><entry /><entry>+ YSD ++I+++++DLLRT ++++ ISEN+KKAI++TEDEHF+EHKG+VPKAV RATL</entry></row><row><entry>Sbjct:</entry><entry>108</entry><entry>ITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGK</entry><entry>167</entry></row><row><entry /></row><row><entry>Query:</entry><entry>147</entry><entry>VLGFGEASGGSTLTQQLVKQQVLGDDPTFKRKSKEIVYALALERYMSKDNILCDYLNVSP</entry><entry>206</entry></row><row><entry /><entry /><entry> +G G +SGGSTLTQQL+KQQV+GD PT  RK+ EIV ALALER M+KD IL  YLNV+P</entry></row><row><entry>Sbjct:</entry><entry>168</entry><entry>FVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAP</entry><entry>227</entry></row><row><entry /></row><row><entry>Query:</entry><entry>207</entry><entry>FGRNNKGQNIAGVEEAARGIFGVSAKDLTVPQAAFLAGLPQSPIVYSPYLSTGQLKSEKD</entry><entry>266</entry></row><row><entry /><entry /><entry>FGRNNKGQNIAG  +AA GIFGV A  LTVPQAAFLAGLPQSPI YSPY +TG+LKS++D</entry></row><row><entry>Sbjct:</entry><entry>228</entry><entry>FGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDED</entry><entry>287</entry></row><row><entry /></row><row><entry>Query:</entry><entry>267</entry><entry>MAYGIKRQQNVLFNMYRTGVLSKKEYEDYKAYPIQKDFIQPGSAIVNNHDYLYYTVLADA</entry><entry>326</entry></row><row><entry /><entry /><entry>+  G++R + VL++MYRTG LSK EY  YK Y +++DF+  G+    + DYLY+T LA+A</entry></row><row><entry>Sbjct:</entry><entry>288</entry><entry>LEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEA</entry><entry>347</entry></row><row><entry /></row><row><entry>Query:</entry><entry>327</entry><entry>KKAMYSYLIKRDKVSSRDLKNDETKAAYEERALTELQQGGYTITTTINKPIYNAMQTAAA</entry><entry>386</entry></row><row><entry /><entry /><entry>++ MY YL +RD VS+++LKN+ T+  Y + A  E++ GGY ITTTI++ I++AMQ+A A</entry></row><row><entry>Sbjct:</entry><entry>348</entry><entry>QERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVA</entry><entry>407</entry></row><row><entry /></row><row><entry>Query:</entry><entry>387</entry><entry>QFGGLLDDGTGTVQMGNVLTDNATGAVLGFVGGRDYALNQNNHAFNTVRSPGSSIKPIIA</entry><entry>446</entry></row><row><entry /><entry /><entry> +G LLDDGTG V++GNVL DN TGA+LGFVGGR+Y  NQNNHAF+T RSP S+ KP++A</entry></row><row><entry>Sbjct:</entry><entry>408</entry><entry>DYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLA</entry><entry>467</entry></row><row><entry /></row><row><entry>Query:</entry><entry>447</entry><entry>YGPAIDQGLMGSASVLSNYPTTYSSGQKIMHADSEGTAMMPLQEALNTSWNIPAFWTQKL</entry><entry>506</entry></row><row><entry /><entry /><entry>YG AIDQGLMGS ++LSNYPT +++G  IM+A+S+GT MM L EALN SWNIPA+WT ++</entry></row><row><entry>Sbjct:</entry><entry>468</entry><entry>YGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRM</entry><entry>527</entry></row><row><entry /></row><row><entry>Query:</entry><entry>507</entry><entry>LREKGVDVENYMTKMGYKIADYSIESLPLGGGIEVSVAQQTNAYQMLSNNGLYQKQYIVD</entry><entry>566</entry></row><row><entry /><entry /><entry>LRE GVDV+ YM KMGY+I +Y IESLP+GGGIEV+VAQ TN YQ L+NNG+Y +++++</entry></row><row><entry>Sbjct:</entry><entry>528</entry><entry>LRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVIS</entry><entry>587</entry></row><row><entry /></row><row><entry>Query:</entry><entry>567</entry><entry>KITASDGTVVYKHENKPIRIFSAATATILQELLRGPITSGATTTFKNRLAAINPWLANAD</entry><entry>626</entry></row><row><entry /><entry /><entry>KI A+DG VVY++++KP++++S ATATI+Q LLR  ++S  TTTFK+ L ++NP LANAD</entry></row><row><entry>Sbjct:</entry><entry>588</entry><entry>KIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANAD</entry><entry>647</entry></row><row><entry /></row><row><entry>Query:</entry><entry>627</entry><entry>WIGKTGTTENYTDVWLVLSTPKVTLGGWAGHDDNTSLAPLTGYNNNSNYLAYLANAINQA</entry><entry>686</entry></row><row><entry /><entry /><entry>WIGKTGTT    ++WL+LSTP++TLGGW GHDDN SL+   GY+NNSNY+A+L NAI QA</entry></row><row><entry>Sbjct:</entry><entry>648</entry><entry>WIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQA</entry><entry>707</entry></row><row><entry /></row><row><entry>Query:</entry><entry>687</entry><entry>DPNVIGVGQRFNLDPGVIKANVLKSTGLQPGTVNVNGHTFSVGGEMTTSLWSQK-GPGAM</entry><entry>745</entry></row><row><entry /><entry /><entry> P++ G  +RF LDP V+K+ VLKSTG +PG V+V G    V G   TS W+ K G  A</entry></row><row><entry>Sbjct:</entry><entry>708</entry><entry>SPSIWG-NERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPAT</entry><entry>766</entry></row><row><entry /></row><row><entry>Query:</entry><entry>746</entry><entry>TYRFAIGGTDADYQKAWGN</entry><entry>764</entry></row><row><entry /><entry /><entry>+YRFAIGG+DADYQ AW +</entry></row><row><entry>Sbjct:</entry><entry>767</entry><entry>SYRFAIGGSDADYQNAWSS</entry><entry>785</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00391" num="00391"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 531/760 (69%), Positives = 639/760 (83%), Gaps = 3/760 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>KKLNSSKLGDYTPLEFGSIFLRIVKLLSDFIYVIILLFVMLGVGLAVGYLASQVDSVKVP</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>K+++  +LG    L+ G + LR ++LLS+F Y++I LF M+G G+A GYLASQ++SVKVP</entry></row><row><entry>Sbjct:</entry><entry>13</entry><entry>KRISHQRLG---LLDLGPVLLRTLRLLSNFFYIVIFLFGMMGFGMAFGYLASQIESVKVP</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>SKNSLVTQVNTLTRVSRLTYSDKSQISEIATDLQRTPVAKDAISDNIKKAIIATEDENFN</entry><entry>125</entry></row><row><entry /><entry /><entry>SK SLV QV +LT +S++ YSD S IS + TDL RTPVA DAIS+NIKKAI++TEDE+F</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>SKESLVKQVESLTMISQMNYSDNSLISTLDTDLLRTPVANDAISENIKKAIVSTEDEHFQ</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>DHKGVVPKAVLRAAAGSVLGFGESSGGSTLTQQLLKQQILGDDPSFKRKSKEIIYALALE</entry><entry>185</entry></row><row><entry /><entry /><entry>+HKG+VPKAV RA   SVLGFGE+SGGSTLTQQL+KQQ+LGDDP+FKRKSKEI+YALALE</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>EHKGIVPKAVFRATLASVLGFGEASGGSTLTQQLVKQQVLGDDPTFKRKSKEIVYALALE</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>RYMDKDSILSDYLNVSPFGRNNKGQNIAGIEEAAQGIFGVSAKDLTIPQAAFLAGLPQSP</entry><entry>245</entry></row><row><entry /><entry /><entry>RYM KD+IL DYLNVSPFGRNNKGQNIAG+EEAA+GIFGVSAKDLT+PQAAFLAGLPQSP</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>RYMSKDNILCDYLNVSPFGRNNKGQNIAGVEEAARGIFGVSAKDLTVPQAAFLAGLPQSP</entry><entry>249</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>IVYSPYTADAQLKSDKDLSFGIKRQKNVLYNMYRTRALTKDEYKSYKDYDIKKDFIKPAV</entry><entry>305</entry></row><row><entry /><entry /><entry>IVYSPY +  QLKS+KD+++GIKRQ+NVL+NMYRT  L+K EY+ YK Y I+KDFI+P</entry></row><row><entry>Sbjct:</entry><entry>250</entry><entry>IVYSPYLSTGQLKSEKDMAYGIKRQQNVLFNMYRTGVLSKKEYEDYKAYPIQKDFIQPGS</entry><entry>309</entry></row><row><entry /></row><row><entry>Query:</entry><entry>306</entry><entry>ATTNHHDYLYYSALSEAQKVMYNYLIKKDNVSEHDLKNDETRATYRHRAIEEIQQGGYTI</entry><entry>365</entry></row><row><entry /><entry /><entry>A  N+HDYLYY+ L++A+K MY+YLIK+D VS  DLKNDET+A Y  RA+ E+QQGGYTI</entry></row><row><entry>Sbjct:</entry><entry>310</entry><entry>AIVNNHDYLYYTVLADAKKAMYSYLIKRDKVSSRDLKNDETKAAYEERALTELQQGGYTI</entry><entry>369</entry></row><row><entry /></row><row><entry>Query:</entry><entry>366</entry><entry>KTTINKSVYQAMQDAAAQYGGLLDDGTGKVQMGNVLTDNSSGAIIGFIGGRNYSENQNNH</entry><entry>425</entry></row><row><entry /><entry /><entry> TTINK +Y AMQ AAAQ+GGLLDDGTG VQMGNVLTDN++GA++GF+GGR+Y+ NQNNH</entry></row><row><entry>Sbjct:</entry><entry>370</entry><entry>TTTINKPIYNAMQTAAAQFGGLLDDGTGTVQMGNVLTDNATGAVLGFVGGRDYALNQNNH</entry><entry>429</entry></row><row><entry /></row><row><entry>Query:</entry><entry>426</entry><entry>AFDTARSPGSSIKPILPYGIAIDQGMLGSGSVLSNYPTTYSSGEKIMHADEEGTAMVNLQ</entry><entry>485</entry></row><row><entry /><entry /><entry>AF+T RSPGSSIKPI+ YG AIDQG++GS SVLSNYPTTYSSG+KIMHAD EGTAM+ LQ</entry></row><row><entry>Sbjct:</entry><entry>430</entry><entry>AFNTVRSPGSSIKPIIAYGPAIDQGLMGSASVLSNYPTTYSSGQKIMHADSEGTAMMPLQ</entry><entry>489</entry></row><row><entry /></row><row><entry>Query:</entry><entry>486</entry><entry>ESLDISWNIPAFWTYKMLRDRGVDVKNYMEKLDYPIENFGIESLPLGGGIDTSVAQQTNL</entry><entry>545</entry></row><row><entry /><entry /><entry>E+L+ SWNIPAFWT K+LR++GVDV+NYM K+ Y I ++ IESLPLGGGI+ SVAQQTN</entry></row><row><entry>Sbjct:</entry><entry>490</entry><entry>EALNTSWNIPAFWTQKLLREKGVDVENYMTKMGYKIADYSIESLPLGGGIEVSVAQQTNA</entry><entry>549</entry></row><row><entry /></row><row><entry>Query:</entry><entry>546</entry><entry>YQMIANGGVYHKQYMIESIEDSNGKVIYNHESKPVRVFSKATATILQQLLHGPINSGKTT</entry><entry>605</entry></row><row><entry /><entry /><entry>YQM++N G+Y KQY+++ I  S+G V+Y HE+KP+R+FS ATATILQ+LL GPI SG TT</entry></row><row><entry>Sbjct:</entry><entry>550</entry><entry>YQMLSNNGLYQKQYIVDKITASDGTVVYKHENKPIRIFSAATATILQELLRGPITSGATT</entry><entry>609</entry></row><row><entry /></row><row><entry>Query:</entry><entry>606</entry><entry>TFKNRLQGLNSGLAGVDWIGKTGTTNSTSDVWLMLSTPKVTLGGWAGHDNNASLAKLTGY</entry><entry>665</entry></row><row><entry /><entry /><entry>TFKNRL  +N  LA  DWIGKTGTT + +DVWL+LSTPKVTLGGWAGHD+N SLA LTGY</entry></row><row><entry>Sbjct:</entry><entry>610</entry><entry>TFKNRLAAINPWLANADWIGKTGTTENYTDVWLVLSTPKVTLGGWAGHDDNTSLAPLTGY</entry><entry>669</entry></row><row><entry /></row><row><entry>Query:</entry><entry>666</entry><entry>NNNANYMAHLVNAINNADGNTFGKSERFRLDDSVIKAKVLKSTGLQPGVVTVNGRRITVG</entry><entry>725</entry></row><row><entry /><entry /><entry>NNN+NY+A+L NAIN AD N  G  +RF LD  VIKA VLKSTGLQPG V VNG   +VG</entry></row><row><entry>Sbjct:</entry><entry>670</entry><entry>NNNSNYLAYLANAINQADPNVIGVGQRFNLDPGVIKANVLKSTGLQPGTVNVNGHTFSVG</entry><entry>729</entry></row><row><entry /></row><row><entry>Query:</entry><entry>726</entry><entry>GESTTSYWAKNGPGTMTYRFAIGGTDSDYQKAWSTLGGKR</entry><entry>765</entry></row><row><entry /><entry /><entry>GE TTS W++ GPG MTYRFAIGGTD+DYQKAW   G ++</entry></row><row><entry>Sbjct:</entry><entry>730</entry><entry>GEMTTSLWSQKGPGAMTYRFAIGGTDADYQKAWGNFGFRK</entry><entry>769</entry></row></tbody></tgroup></table></tables>

SEQ ID 374 (GBS64d) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 120</figref> (lane 24; MW 107 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 120</figref> (lane 5-7; MW 82 kDa) and in <figref idrefs="DRAWINGS">FIG. 179</figref> (lane 2; MW 82 kDa).

GBS64d-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 231</figref>, lane 7-8.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 113

A DNA sequence (GBSx0116) was identified in <i>S. agalactiae </i>&lt;SEQ ID 377&gt; which encodes the amino acid sequence &lt;SEQ ID 378&gt;. This protein is predicted to be DNA-dependent RNA polymerase subunit beta (rpoB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00392" num="00392"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3505(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00393" num="00393"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB56706 GB: Y16468 DNA-dependent RNA polymerase subunit beta</entry><entry /></row><row><entry>[<i>Listeria monocytogenes</i>]</entry></row><row><entry>Identities = 814/1173 (69%), Positives = 978/1173 (82%), Gaps = 17/1173 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>AGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDAGLKEVFEDVLPISNFTDT</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+GH+V+YG+HRTRRSF+RI EVL+LPNLIEIQT S+Q FLD GL+E+F D+ PI +F</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFLDEGLREMFRDISPIEDFAGN</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>MDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMTE</entry><entry>121</entry></row><row><entry /><entry /><entry>+ LEF+ Y+L EPKY++EE++  DA+Y+AP+ V  RL+NKETGE+K QEVF GDFP+MTE</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>LSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLINKETGEVKDQEVFMGDFPLMTE</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>MGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDAKDIAY</entry><entry>181</entry></row><row><entry /><entry /><entry>MGTFIING ER+IVSQLVRSPGVYFN K+DKNGK G+GSTVIPNRGAWLE ETDAKD+ +</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>MGTFIINGAERVIVSQLVRSPGVYFNGKLDKNGKKGFGSTVIPNRGAWLEYETDAKDVVH</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>TRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVRNTIEKDIHKNPSDSRTDEALKEI</entry><entry>241</entry></row><row><entry /><entry /><entry> RIDRTRK+P T L+RALGF  D EI+D+ GD++ +RNT+EKD   N      ++AL EI</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>VRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRNTLEKDNTDN-----AEKALLEI</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>YERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGRYKINKKLNLKTRLLNQTIAENLVD</entry><entry>301</entry></row><row><entry /><entry /><entry>YERLRPGEP T D++RSLLV+RFFDP+RYDLA+VGRYKINKKL+LK RL NQT+AE LVD</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>YERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRYKINKKLHLKNRLFNQTLAETLVD</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>GETGEILVEAGTVMTRDVIDSIAEHIDGDLNKFVYTPNDYAVVTEPVILQKFKVVAPTDP</entry><entry>361</entry></row><row><entry /><entry /><entry> ETGEI+   G ++ R  +D I  +++ +      P D  V+ + V++Q  K+ AP D</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>PETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRPTD-GVMEDSVLVQSIKIYAPNDE</entry><entry>358</entry></row><row><entry /></row><row><entry>Query:</entry><entry>362</entry><entry>DRVVTIVGNSNPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGELLA</entry><entry>421</entry></row><row><entry /><entry /><entry>++ + I+GN+  E+ V+ +TP+DI++ +SYF NL  G+G  DDIDHLGNRR+R+VGELL</entry></row><row><entry>Sbjct:</entry><entry>359</entry><entry>EKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQ</entry><entry>418</entry></row><row><entry /></row><row><entry>Query:</entry><entry>422</entry><entry>NQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPL</entry><entry>481</entry></row><row><entry /><entry /><entry>NQFRIGL+RMER VRERMS+QD   +TPQQ+INIRPV A++KEFFGSSQLSQFMDQ NPL</entry></row><row><entry>Sbjct:</entry><entry>419</entry><entry>NQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPL</entry><entry>478</entry></row><row><entry /></row><row><entry>Query:</entry><entry>482</entry><entry>SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHL</entry><entry>541</entry></row><row><entry /><entry /><entry> EL+HKRRLSALGPGGLTR+RAGYEVRDVHY+HYGRMCPIETPEGPNIGLIN+LSSF  +</entry></row><row><entry>Sbjct:</entry><entry>479</entry><entry>GELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKV</entry><entry>538</entry></row><row><entry /></row><row><entry>Query:</entry><entry>542</entry><entry>NKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGRHQ</entry><entry>601</entry></row><row><entry /><entry /><entry>NK+GFI+TPYR+VD  T  VT++I +LTADEED + VAQANSKL+E GTF EE VM R +</entry></row><row><entry>Sbjct:</entry><entry>539</entry><entry>NKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFR</entry><entry>598</entry></row><row><entry /></row><row><entry>Query:</entry><entry>602</entry><entry>GNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPY</entry><entry>661</entry></row><row><entry /><entry /><entry>  N       +D++DVSPKQVV+VATACIPFLENDDSNRALMGANMQRQAVPL+ P+AP+</entry></row><row><entry>Sbjct:</entry><entry>599</entry><entry>SENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPF</entry><entry>658</entry></row><row><entry /></row><row><entry>Query:</entry><entry>662</entry><entry>VGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRRED--------GSLDVYHVQKFRR</entry><entry>713</entry></row><row><entry /><entry /><entry>VGTGME+ +A DSGAAV AKHDG V   +A ++ VRR          G +D Y ++KF R</entry></row><row><entry>Sbjct:</entry><entry>659</entry><entry>VGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVR</entry><entry>718</entry></row><row><entry /></row><row><entry>Query:</entry><entry>714</entry><entry>SNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIM</entry><entry>773</entry></row><row><entry /><entry /><entry>SN GT YNQR  V  GD V KG+ + +GPSM++GE+ALG+N +VA+MTW+GYN+EDA+IM</entry></row><row><entry>Sbjct:</entry><entry>719</entry><entry>SNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIM</entry><entry>778</entry></row><row><entry /></row><row><entry>Query:</entry><entry>774</entry><entry>SERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVK</entry><entry>833</entry></row><row><entry /><entry /><entry>SERLVK+DVYTS+H+EEFESE RDTKLGPEE+TR+IPNVGED+LRDLDE GIIR+GAEVK</entry></row><row><entry>Sbjct:</entry><entry>779</entry><entry>SERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVK</entry><entry>838</entry></row><row><entry /></row><row><entry>Query:</entry><entry>834</entry><entry>EGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRAN</entry><entry>893</entry></row><row><entry /><entry /><entry>+ D+LVGKVTPKG  +L+AEERLLHAIFG+K+REVRDTSLRVPHGG G+V DVKIFTR</entry></row><row><entry>Sbjct:</entry><entry>839</entry><entry>DNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREA</entry><entry>898</entry></row><row><entry /></row><row><entry>Query:</entry><entry>894</entry><entry>GDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIML</entry><entry>953</entry></row><row><entry /><entry /><entry>GDEL  GVN LVRVYI QKRKI  GDKMAGRHGNKGV+SRI+P EDMP++PDGTPVDIML</entry></row><row><entry>Sbjct:</entry><entry>899</entry><entry>GDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIML</entry><entry>958</entry></row><row><entry /></row><row><entry>Query:</entry><entry>954</entry><entry>NPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMDSDAKTVL</entry><entry>1013</entry></row><row><entry /><entry /><entry>NPLGVPSRMNIGQV+ELHLGMAAR LGIH+ATPVFDGA+ ED+W TV+EAGM DAKT+L</entry></row><row><entry>Sbjct:</entry><entry>959</entry><entry>NPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARDAKTIL</entry><entry>1018</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1014</entry><entry>YDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGE</entry><entry>1073</entry></row><row><entry /><entry /><entry>YDGR+GE FDNR+SVGVMYMIKL HMVDDKLHARS GPYSLVTQQPLGGKAQFGGQRFGE</entry></row><row><entry>Sbjct:</entry><entry>1019</entry><entry>YDGRSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE</entry><entry>1078</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1074</entry><entry>MEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQS</entry><entry>1133</entry></row><row><entry /><entry /><entry>MEVWALEAYGA+  LQEILT KSDDV GR+K YEAI KG+ +P+PGVPESF+VL+KELQS</entry></row><row><entry>Sbjct:</entry><entry>1079</entry><entry>MEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQS</entry><entry>1138</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1134</entry><entry>LGLDMRVLDEDDNEVELRDLDEGEDDDVMHVDD</entry><entry>1166</entry></row><row><entry /><entry /><entry>LG+D+++L  D+ E+E+RD+D   DDD  + +D</entry></row><row><entry>Sbjct:</entry><entry>1139</entry><entry>LGMDVKMLSADEEEIEMRDMD---DDDFTNQND</entry><entry>1168</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 379&gt; which encodes the amino acid sequence &lt;SEQ ID 380&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00394" num="00394"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3392(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00395" num="00395"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Identities = 1129/1190 (94%), Positives = 1168/1190 (97%), Gaps = 3/1190 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDAGLKEVFEDVLPISNFTD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+AGHEV+YGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLD+GLKEVFEDVLPISNFTD</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDSGLKEVFEDVLPISNFTD</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TMDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT</entry><entry>120</entry></row><row><entry /><entry /><entry>TM+LEFVGYE KEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDAKDIA</entry><entry>180</entry></row><row><entry /><entry /><entry>EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETD+KDIA</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDSKDIA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVRNTIEKDIHKNPSDSRTDEALKE</entry><entry>240</entry></row><row><entry /><entry /><entry>YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFG+S+LVRNTIEKDIHKNPSDSRTDEALKE</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVRNTIEKDIHKNPSDSRTDEALKE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>IYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGRYKINKKLNLKTRLLNQTIAENLV</entry><entry>300</entry></row><row><entry /><entry /><entry>IYERLRPGEPKTADSSRSLL+ARFFD RRYDLAAVGRYK+NKKLN+KTRLLNQ IAENLV</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>IYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGRYKVNKKLNIKTRLLNQIIAENLV</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>DGETGEILVEAGTVMTRDVIDSIAEHIDGDLNKFVYTPNDYAVVTEPVILQKFKVVAPTD</entry><entry>360</entry></row><row><entry /><entry /><entry>D ETGEILVEAGT MTR VI+SI EH+DGDLNKFVYTPNDYAVVTEPV+LQKFKVV+P D</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>DAETGEILVEAGTEMTRSVIESIEEHLDGDLNKFVYTPNDYAVVTEPVVLQKFKVVSPID</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>PDRVVTIVGNSNPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGELL</entry><entry>420</entry></row><row><entry /><entry /><entry>PDRVVTIVGN+NP+DKVRALTPADILAEMSYFLNLAEG+GKVDDIDHLGNRRIRAVGELL</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>PDRVVTIVGNANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGELL</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>ANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP</entry><entry>480</entry></row><row><entry /><entry /><entry>ANQFRIGLARMERNVRERMSVQDN+VLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>ANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH</entry><entry>540</entry></row><row><entry /><entry /><entry>LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>LNKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGRH</entry><entry>600</entry></row><row><entry /><entry /><entry>LNKYGFIQTPYRKVDR+TG VTNEIVWLTADEEDE+TVAQANSKLNEDGTFAEEIVMGRH</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>LNKYGFIQTPYRKVDRATGTVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGRH</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>QGNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAP</entry><entry>660</entry></row><row><entry /><entry /><entry>QGNNQEF +S+VDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPRAP</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>QGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAP</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>661</entry><entry>YVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLDVYHVQKFRRSNSGTAY</entry><entry>720</entry></row><row><entry /><entry /><entry>YVGTGMEYQAAHDSGAAVIA+ +G+V+FSDAEKVE+RR+DGSLDVYH+ KFRRSNSGTAY</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>YVGTGMEYQAAHDSGAAVIAQQNGKVVFSDAEKVEIRRQDGSLDVYHITKFRRSNSGTAY</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>721</entry><entry>NQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE</entry><entry>780</entry></row><row><entry /><entry /><entry>NQRTLVKVGD+VEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE</entry></row><row><entry>Sbjct:</entry><entry>721</entry><entry>NQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE</entry><entry>780</entry></row><row><entry /></row><row><entry>Query:</entry><entry>781</entry><entry>DVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVG</entry><entry>840</entry></row><row><entry /><entry /><entry>DVYTSVHLEEFESETRDTKLGPEEITREIPNVGE++L+DLDEMGIIRIGAEVKEGDILVG</entry></row><row><entry>Sbjct:</entry><entry>781</entry><entry>DVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEVKEGDILVG</entry><entry>840</entry></row><row><entry /></row><row><entry>Query:</entry><entry>841</entry><entry>KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRANGDELQSG</entry><entry>900</entry></row><row><entry /><entry /><entry>KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDG+VRDVKIFTRANGDELQSG</entry></row><row><entry>Sbjct:</entry><entry>841</entry><entry>KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVIKFTRANGDELQSG</entry><entry>900</entry></row><row><entry /></row><row><entry>Query:</entry><entry>901</entry><entry>VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS</entry><entry>960</entry></row><row><entry /><entry /><entry>VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS</entry></row><row><entry>Sbjct:</entry><entry>901</entry><entry>VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS</entry><entry>960</entry></row><row><entry /></row><row><entry>Query:</entry><entry>961</entry><entry>RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMDSDAKTVLYDGRTGE</entry><entry>1020</entry></row><row><entry /><entry /><entry>RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW+TV+EAGMDSDAKTVLYDGRTGE</entry></row><row><entry>Sbjct:</entry><entry>961</entry><entry>RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGMDSDAKTVLYDGRTGE</entry><entry>1020</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1021</entry><entry>PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE</entry><entry>1080</entry></row><row><entry /><entry /><entry>PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE</entry></row><row><entry>Sbjct:</entry><entry>1021</entry><entry>PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE</entry><entry>1080</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1081</entry><entry>AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRV</entry><entry>1140</entry></row><row><entry /><entry /><entry>AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRV</entry></row><row><entry>Sbjct:</entry><entry>1081</entry><entry>AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESERVLVKELQSLGLDNRV</entry><entry>1140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1141</entry><entry>LDEDDNEVELRDLDEGEDDDVMHVDDLEKARVKQEAEEKQAEQVSEVVQE</entry><entry>1190</entry></row><row><entry /><entry /><entry>LDEDDNEVELRDLDEGEDDD+MHVDDLEKAR KQ  E    ++VSE   E</entry></row><row><entry>Sbjct:</entry><entry>1141</entry><entry>LDEDDNEVELRDLDEGEDDDIMHVDDLEKAREKQAQE---TQEVSETTDE</entry><entry>1187</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 114

A DNA sequence (GBSx0118) was identified in <i>S. agalactiae </i>&lt;SEQ ID 381&gt; which encodes the amino acid sequence &lt;SEQ ID 382&gt;. This protein is predicted to be DNA-directed RNA polymerase, beta subunit (rpoC). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00396" num="00396"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1892 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 383&gt; which encodes the amino acid sequence &lt;SEQ ID 384&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00397" num="00397"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2128 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00398" num="00398"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Identities = 1148/1205 (95%), Positives = 1177/1205 (97%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC</entry><entry>70</entry><entry /></row><row><entry /><entry /><entry>VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>71</entry><entry>ACGKYKRIRYKGIICDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM</entry><entry>130</entry></row><row><entry /><entry /><entry>ACGKYKRIRYKGI+CDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ACGKYKRIRYKGIVCDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>131</entry><entry>SPRALEEVIYFAAYVVIDPMDTPLEPKSLLTEREYREKLQEYGYGSFVAKMGAEAIQDLL</entry><entry>190</entry></row><row><entry /><entry /><entry>SPRALEEVIYFAAYVVIDP DTPLEPKSLLTEREYREKLQEYG+GSFVAKMGAEAIQDLL</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SPRALEEVIYFAAYVVIDPKDTPLEPKSLLTEREYREKLQEYGHGSFVAKMGAEAIQDLL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>191</entry><entry>KRVDLDAEIAVLKEELKSATGQKRVKAVRRLDVLDAFKKSGNKPEWMVLNILPVIPPDLR</entry><entry>250</entry></row><row><entry /><entry /><entry>KRVDL AEIA LKEELKSA+GQKR+KAVRRLDVLDAF KSGNKPEWMVLNILPVIPPDLR</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KRVDLAAEIAELKEELKSASGQKRIKAVRRLDVLDAFNKSGNKPEWMVLNILPVIPPDLR</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>251</entry><entry>PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG</entry><entry>310</entry></row><row><entry /><entry /><entry>PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>311</entry><entry>RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR</entry><entry>370</entry></row><row><entry /><entry /><entry>RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>371</entry><entry>EMAIELFKPFVMREIVARDLAGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH</entry><entry>430</entry></row><row><entry /><entry /><entry>EMAIELFKPFVMREIVA++ AGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>EMAIELFKPFVMREIVAKEYAGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>431</entry><entry>RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI</entry><entry>490</entry></row><row><entry /><entry /><entry>RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>491</entry><entry>LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKDHDEAVMAYQNGYVHLHTRVGI</entry><entry>550</entry></row><row><entry /><entry /><entry>LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKD DEAVMAY+NGY HLH+RVGI</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKDKDEAVMAYRNGYAHLHSRVGI</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>551</entry><entry>AVDSMPNKPWTEEQKHKIMVTTVGKILFNDIMPEDLPYLIEPNNANLTEKTPDKYFLEPG</entry><entry>610</entry></row><row><entry /><entry /><entry>AVDSMPNKPW + Q+HKIMVTTVGKILFNDIMPEDLPYL EPNNANLTE TPDKYFLEPG</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>AVDSMPNKPWKDNQRHKIMVTTVGKILFNDIMPEDLPYLQEPNNANLTEGTPDKYFLEPG</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>611</entry><entry>QDIQAVIDNLEINIPFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG</entry><entry>670</entry></row><row><entry /><entry /><entry>QDIQ VID L+IN+PFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>QDIQEVIDRLDINVPFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>671</entry><entry>IADIPVIDNKAEIIDAAHHRVEDINKAFRRGLMTEEDRYVAVTTTWREAKEALEKRLIET</entry><entry>730</entry></row><row><entry /><entry /><entry>IADIPVIDNKAEIIDAAHHRVE+INKAFRRGLMT++DRYVAVTTTWREAKEALEKRLIET</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>IADIPVIDNKAEIIDAAHHRVEEINKAFRRGLMTDDDRYVAVTTTWREAKEALEKRLIET</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>731</entry><entry>QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS</entry><entry>790</entry></row><row><entry /><entry /><entry>QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS</entry></row><row><entry>Sbjct:</entry><entry>721</entry><entry>QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS</entry><entry>780</entry></row><row><entry /></row><row><entry>Query:</entry><entry>791</entry><entry>THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTITAITDGKEVTETL</entry><entry>850</entry></row><row><entry /><entry /><entry>THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGL I AITDGKEVTETL</entry></row><row><entry>Sbjct:</entry><entry>781</entry><entry>THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLLIRAITDGKEVTETL</entry><entry>840</entry></row><row><entry /></row><row><entry>Query:</entry><entry>851</entry><entry>EERLIGRYTKKSIKHPETGEILVGADTLITEDMAAKVVKAGVEEVTIRSVFTCNTRHGVC</entry><entry>910</entry></row><row><entry /><entry /><entry>EERL GRYT+KS+KHPETGE+L+GAD LITEDMA K+V AGVEEVTIRSVFTC TRHGVC</entry></row><row><entry>Sbjct:</entry><entry>841</entry><entry>EERLQGRYTRKSVKHPETGEVLIGADQLITEDMARKIVDAGVEEVTIRSVFTCATRHGVC</entry><entry>900</entry></row><row><entry /></row><row><entry>Query:</entry><entry>911</entry><entry>RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE</entry><entry>970</entry></row><row><entry /><entry /><entry>RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE</entry></row><row><entry>Sbjct:</entry><entry>901</entry><entry>RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE</entry><entry>960</entry></row><row><entry /></row><row><entry>Query:</entry><entry>971</entry><entry>IFEARNPKGEAVITEVKGEVVAIEEDSSTRTKKVFVKGQTGEGEYVVPFTARMKVEVGDE</entry><entry>1030</entry></row><row><entry /><entry /><entry>IFEARNPKGEAVITEVKG VV IEED+STRTKKV+V+G+TG GEYV+PFTARMKVEVGDE</entry></row><row><entry>Sbjct:</entry><entry>961</entry><entry>IFEARNPKGEAVITEVKGNVVEIEEDASTRTKKVYVQGKTGMGEYVIPFTARMKVEVGDE</entry><entry>1020</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1031</entry><entry>VARGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK</entry><entry>1090</entry></row><row><entry /><entry /><entry>V RGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK</entry></row><row><entry>Sbjct:</entry><entry>1021</entry><entry>VNRGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK</entry><entry>1080</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1091</entry><entry>VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA</entry><entry>1150</entry></row><row><entry /><entry /><entry>VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA</entry></row><row><entry>Sbjct:</entry><entry>1081</entry><entry>VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA</entry><entry>1140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1151</entry><entry>SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEPLAVNEVEIIEGT</entry><entry>1210</entry></row><row><entry /><entry /><entry>SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEP A+NE+E+I+ T</entry></row><row><entry>Sbjct:</entry><entry>1141</entry><entry>SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEPQAMNEIEVIDHT</entry><entry>1200</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1211</entry><entry>PVDAE</entry><entry>1215</entry></row><row><entry /><entry /><entry> V AE</entry></row><row><entry>Sbjct:</entry><entry>1201</entry><entry>EVSAE</entry><entry>1205</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 115

A DNA sequence (GBSx0120) was identified in <i>S. agalactiae </i>&lt;SEQ ID 385&gt; which encodes the amino acid sequence &lt;SEQ ID 386&gt;. This protein is predicted to be a DNA binding protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00399" num="00399"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4727(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00400" num="00400"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC45309 GB: U81957 putative DNA binding protein</entry><entry /></row><row><entry>[<i>Streptococcus gordonii</i>]</entry></row><row><entry>Identities = 42/99 (42%), Positives = 75/99 (75%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYQVVKMFGDWEPWWFIEGWEEDITEIAEYDTLSEALLYFQEEWDRGQEKWPYFQSKSSL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MY+VV+M+GD+EPWWF++GWE DI +   ++   +AL +++ +W + + ++  ++S+S L</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MYRVVEMYGDFEPWWFLDGWENDIIQEQRFEKYYDALKFYKIQWLKLETEFKEYKSRSDL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LATFWSIKEKRWCEECDEYLQQYHSLMLLKEWQEIPKEE</entry><entry>99</entry></row><row><entry /><entry /><entry>+  FW+  ++RWCEECD+Y+QQY S++LL++ + IPK +</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>MTVFWNENDQRWCEECDDYVQQYRSIILLEDEKVIPKSK</entry><entry>99</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 387&gt; which encodes the amino acid sequence &lt;SEQ ID 388&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00401" num="00401"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4741(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00402" num="00402"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 61/121 (50%), Positives = 83/121 (68%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYQVVKMFGDWEPWWFIEGWEEDITEIAEYDTLSEALLYFQEEWDRGQEKWPYFQSKSSL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MYQV+KM+GDWEPWWFI+GW++DI +  ++    EAL YF +EW R +  +P + S+ +L</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MYQVIKMYGDWEPWWFIDGWQDDIIDEQQFSDWQEALDYFNQEWQRMKAIFPSYHSQKNL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LATFWSIKEKRWCEECDEYLQQYHSLMLLKEWQEIPKEESIERFEVFNKIAELPSACSLNL</entry><entry>121</entry></row><row><entry /><entry /><entry>LATFW  ++KRWCE+CDE LQQ+HSL+LLK    +P    I  FE  N   ++   C LNL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LATFWEKEDKRWCEDCDEDLQQFHSLLLLKNKDIVPSNNYIPEFEQRNDSPQVAYLCKLNL</entry><entry>121</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 116

A DNA sequence (GBSx0121) was identified in <i>S. agalactiae </i>&lt;SEQ ID 389&gt; which encodes the amino acid sequence &lt;SEQ ID 390&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00403" num="00403"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty= 0.2433(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00404" num="00404"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC45310 GB: U81957 putative ABC transporter subunit ComYA</entry><entry /></row><row><entry>[<i>Streptococcus gordonii</i>]</entry></row><row><entry>Identities = 203/319 (63%), Positives = 255/319 (79%), Gaps = 1/319 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVQSLAKQVIHQAVEVNAQDIYIIPKGDCYELYMRIDDERRFIDVFEFNRMASLISHFKF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MVQ +A+ ++ QA E  AQDIY +PK DCYELYMRI DERRFI  ++F+++A++ISHFKF</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MVQKIAQAIVRQAKEECAQDIYFVPKDDCYELYMRIGDERRFIQTYDFDQLAAVISHFKF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VAGMNVGEKRRSQLGSCDYELSEGRLVSLRLSSVGDYRGQESLVIRILYSGHQDLKYWFD</entry><entry>120</entry></row><row><entry /><entry /><entry>+AGMNVGEKRRSQLGSCDY   + +  S+RLS+VGDYRG ESLVIR+L+    +LK+WF</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LAGMNVGEKRRSQLGSCDYRYDD-KETSIRLSTVGDYRGYESLVIRLLHDEETELKFWFT</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NIKQMKEVLGIRGLYLFSGPVGSGKTTLMYQLASEVFKNKQIITIEDPVEIKNDKMLQLQ</entry><entry>180</entry></row><row><entry /><entry /><entry>+  +++E    RGLYLFSGPVGSGKTTLM+QLA   FK +Q+++IEDPVEIK + MLQLQ</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>HFPELREKFKDRGLYLFSGPVGSGKTTLMHQLAQLKFKGQQVMSIEDPVEIKQEDMLQLQ</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LNEDIGMTYDALIKLSLRHRPDILIIGEIRDQATARAVIRASLTGVMVFSTIHAKSIPGV</entry><entry>240</entry></row><row><entry /><entry /><entry>LNE IG+TY++LIKLSLRHRPD+LIIGEIRD  TARAV+RASLTG  VFSTIHAKSIPGV</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>LNETIGLTYESLIKLSLRHRPDLLIIGEIRDSETARAVVRASLTGATVFSTIHAKSIPGV</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>YDRLIELGVNYQELENSLKLIAYQRLIGGGSLIDFETGNFKKHSSDKWNRQVDILAEEGH</entry><entry>300</entry></row><row><entry /><entry /><entry>Y+RL+ELGV+ +EL+  L+ I YQRLIGGG +IDF + N+++H    WN+Q+D L   GH</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>YERLLELGVSEEELKIVLQGICYQRLIGGGGVIDFASDNYQEHEPTVWNQQIDQLLAAGH</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>ISKKQAQVEKIIPQETTES</entry><entry>319</entry></row><row><entry /><entry /><entry>I  +QA+ EKI  Q+   S</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>IHPEQAEAEKIRNQQAKTS</entry><entry>318</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 391&gt; which encodes the amino acid sequence &lt;SEQ ID 392&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00405" num="00405"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1846(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00406" num="00406"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 207/312 (66%), Positives = 257/312 (82%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVQSLAKQVIHQAVEVNAQDIYIIPKGDCYELYMRIDDERRFIDVFEFNRMASLISHFKF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MVQ+LAK ++ +A +V+AQDIYI+P+ D Y+L++RI DERR +DV++ +RMA LISHFKF</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MVQALAKAILAKAEQVHAQDIYILPRADQYDLFLRIGDERRLVDVYQSDRMAPLISHFKF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VAGMNVGEKRRSQLGSCDYELSEGRLVSLRLSSVGDYRGQESLVIRILYSGHQDLKYWFD</entry><entry>120</entry></row><row><entry /><entry /><entry>VAGM VGEKRR Q+GSCDY+LS+ + +SLRLSSVGDYRGQESLVIR+L+  ++ + YWFD</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VAGMIVGEKRRCQVGSCDYKLSKDKQLSLRLSSVGDYRGQESLVIRLLHHQNKSVHYWFD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NIKQMKEVLGIRGLYLFSGPVGSGKTTLMYQLASEVFKNKQIITIEDPVEIKNDKMLQLQ</entry><entry>180</entry></row><row><entry /><entry /><entry> + ++   +G RGLYLF+GPVGSGKTTLMYQL S   +  Q+I+IEDPVEIKN ++LQLQ</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GLTKVANQVGGRGLYLFAGPVGSGKTTLMYQLISNYHQEAQVISIEDPVEIKNHQILQLQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LNEDIGMTYDALIKLSLRHRPDILIIGEIRDQATARAVIRASLTGVMVFSTIHAKSIPGV</entry><entry>240</entry></row><row><entry /><entry /><entry>+N+DIGMTYD LIKLSLRHRPDIL+IGEIRD  TARAVIRASLTG MVFST+HAKSI GV</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VNDDIGMTYDNLIKLSLRHRPDILVIGEIRDSQTARAVIRASLTGAMVFSTVHAKSISGV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>YDRLIELGVNYQELENSLKLIAYQRLIGGGSLIDFETGNFKKHSSDKWNRQVDILAEEGH</entry><entry>300</entry></row><row><entry /><entry /><entry>Y RL+ELGV   EL N L LIAYQRL+ GG+LID     F+ +SS  WN+Q+D L E GH</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YARLLELGVTKAELSNCLALIAYQRLLNGGALIDSTQNEFEYYSSSNWNQQIDQLLEAGH</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>ISKKQAQVEKII</entry><entry>312</entry></row><row><entry /><entry /><entry>++ KQA++EKII</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LNPKQAKLEKII</entry><entry>312</entry></row></tbody></tgroup></table></tables>

SEQ ID 390 (GBS63) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 5</figref> (lane 5; MW 39 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 13</figref> (lane 2; MW 64 kDa).

The GBS63-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 101A</figref>; see also <figref idrefs="DRAWINGS">FIG. 191</figref>, lane 3) and used to immunise mice (lane 1 product; 20 μg/mouse). The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 101B</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 101C</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 117

A DNA sequence (GBSx0122) was identified in <i>S. agalactiae </i>&lt;SEQ ID 393&gt; which encodes the amino acid sequence &lt;SEQ ID 394&gt;. This protein is predicted to be competence protein (mshG). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00407" num="00407"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −14.65</entry><entry>Transmembrane</entry><entry>123-139 (113-144)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −13.53</entry><entry>Transmembrane</entry><entry>272-288 (264-295)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.55</entry><entry>Transmembrane</entry><entry>  79-95 (75-102)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.00</entry><entry>Transmembrane</entry><entry>146-162 (146-162)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6859(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9489&gt; which encodes amino acid sequence &lt;SEQ ID 9490&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00408" num="00408"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC45311 GB: U81957 putative ABC transporter subunit ComYB</entry><entry /></row><row><entry>[<i>Streptococcus gordonii</i>]</entry></row><row><entry>Identities = 161/280 (57%), Positives = 219/280 (77%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>19</entry><entry>MNKALLEGKDLSKMLGELGFSDTVITQVALADLHGNISRSLLKIESYLANLLLVRKKVIE</entry><entry>78</entry><entry /></row><row><entry /><entry /><entry>M + L  G+  S+++  LGFSD V+TQ++LA+LHGN+S +LLKIE YL NL  V+KK+IE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRQGLANGQAFSEIMASLGFSDAVVTQLSLAELHGNLSLALLKIEEYLDNLAKVKKKLIE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>79</entry><entry>VATYPLILLSFLVLIMIGLRNYLMPQLGENNFATRLITNVPNIFLLLLAVVLIFSLIFYI</entry><entry>138</entry></row><row><entry /><entry /><entry>VATYP++LL FLVLIMIGLRNYL+PQL   NFAT+LI ++P IFLL + ++L  +   Y+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VATYPMMLLGFLVLIMIGLRNYLLPQLSSQNFATQLIGHLPTIFLLTVLMLLGLTGAIYL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>139</entry><entry>IQKRLSRIKVACFLTTIPLVGSYVKLYLTAYYAREWGNLLSQGIELDQIVKVMQNQKSKL</entry><entry>198</entry></row><row><entry /><entry /><entry>+ K   RI V  FL  +P VGS+V++YLTAYYAREWGN++ QG+EL QI ++MQ Q+S L</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VFKGQKRIPVYSFLARLPFVGSFVRIYLTAYYAREWGNMIGQGLELSQIFQIMQEQRSVL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>199</entry><entry>FREIGYDMEEGFLSGKAFHQKVLDYPFFLTELSLMIEYGQVKAKLGTELDIYADEKWEDF</entry><entry>258</entry></row><row><entry /><entry /><entry>F+EIG D+ +   +G+ F  K+  YPFF  ELSL+IEYG+VK+KLG+EL+IYA + WE+F</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>FQEIGQDLGQALQNGQEFSDKIASYPFFKKELSLIIEYGEVKSKLGSELEIYALKTWEEF</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>259</entry><entry>FTKLARATQLIQPVIFIFVALIIVMIYAAMLLPMYQNMEI</entry><entry>298</entry></row><row><entry /><entry /><entry>F ++ R   LIQP++F+FVAL+IV++YAAMLLP+YQNME+</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>FGRVNRTMNLIQPLVFVFVALMIVLLYAAMLLPLYQNMEV</entry><entry>280</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 395&gt; which encodes the amino acid sequence &lt;SEQ ID 396&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00409" num="00409"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.52</entry><entry>Transmembrane</entry><entry>317-333 (309-339)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.14</entry><entry>Transmembrane</entry><entry>123-139 (119-147)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.95</entry><entry>Transmembrane</entry><entry>164-180 (161-183)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6010(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00410" num="00410"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC45311 GB: U81957 putative ABC transporter subunit ComYB</entry><entry /></row><row><entry>[<i>Streptococcus gordonii</i>]</entry></row><row><entry>Identities = 139/278 (50%), Positives = 207/278 (74%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>63</entry><entry>MEESLLKGQGLADMLSGLGFSDAILTQISLADRHGNIETTLVAIQHYLNQMARIRRKTVE</entry><entry>122</entry><entry /></row><row><entry /><entry /><entry>M + L  GQ  +++++ LGFSDA++TQ+SLA+ HGN+   L+ I+ YL+ +A++++K +E</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRQGLANGQAFSEIMASLGFSDAVVTQLSLAELHGNLSLALLKIEEYLDNLAKVKKKLIE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>VITYPLILLLFLFVMMLGLRRYLVPQLETQNQITYFLNHFPAFFIGFCSGLILLFGMVWL</entry><entry>182</entry></row><row><entry /><entry /><entry>V TYP++LL FL ++M+GLR YL+PQL +QN  T  + H P  F+     L+ L G ++L</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VATYPMMLLGFLVLIMIGLRNYLLPQLSSQNFATQLIGHLPTIFLLTVLMLLGLTGAIYL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>RWRSQSRLKLYSRLSRYPFLGKLLKQYLTSYYAREWGTLIGQGLDLMTILDIMAIEKSSL</entry><entry>242</entry></row><row><entry /><entry /><entry> ++ Q R+ +YS L+R PF+G  ++ YLT+YYAREWG +IGQGL+L  I  IM  ++S L</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VFKGQKRIPVYSFLARLPFVGSFVRIYLTAYYAREWGNMIGQGLELSQIFQIMQEQRSVL</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>MKELAEDIRMSLLEGQAFHIKVATYPFFKKELSLMIEYGEIKSKLGAELEIYAQESWEQF</entry><entry>302</entry></row><row><entry /><entry /><entry> +E+ +D+  +L  GQ F  K+A+YPFFKKELSL+IEYGE+KSKLG+ELEIYA ++WE+F</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>FQEIGQDLGQALQNGQEFSDKIASYPFFKKELSLIIEYGEVKSKLGSELEIYALKTWEEF</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>303</entry><entry>FSQLYQVTQLIQPAIFLVVAVTIVMIYAAILLPIYQNM</entry><entry>340</entry></row><row><entry /><entry /><entry>F ++ +   LIQP +F+ VA+ IV++YAA+LLP+YQNM</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>FGRVNRTMNLIQPLVFVFVALMIVLLYAAMLLPLYQNM</entry><entry>278</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00411" num="00411"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 148/297 (49%), Positives = 209/297 (69%), Gaps = 2/297 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVTFLKRSKLLSDCYTDSMNKALLEGKDLSKMLGELGFSDTVITQVALADLHGNISRSLL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>++ FLKRS+LL   Y   M ++LL+G+ L+ ML  LGFSD ++TQ++LAD HGNI  +L+</entry></row><row><entry>Sbjct:</entry><entry>45</entry><entry>VIAFLKRSQLLQLDYVLKMEESLLKGQGLADMLSGLGFSDAILTQISLADRHGNIETTLV</entry><entry>104</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KIESYLANLLLVRKKVIEVATYPLILLSFLVLIMIGLRNYLMPQLGENNFATRLITNVPN</entry><entry>120</entry></row><row><entry /><entry /><entry> I+ YL  +  +R+K +EV TYPLILL FL ++M+GLR YL+PQL   N  T  + + P</entry></row><row><entry>Sbjct:</entry><entry>105</entry><entry>AIQHYLNQMARIRRKTVEVITYPLILLLFLFVMMLGLRRYLVPQLETQNQITYFLNHFPA</entry><entry>164</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IFL-LLLAVVLIFSLIFYIIQKRLSRIKVACFLTTIPLVGSYVKLYLTAYYAREWGNLLS</entry><entry>179</entry></row><row><entry /><entry /><entry> F+     ++L+F ++ ++  +  SR+K+   L+  P +G  +K YLT+YYAREWG L+</entry></row><row><entry>Sbjct:</entry><entry>165</entry><entry>FFIGFCSGLILLFGMV-WLRWRSQSRLKLYSRLSRYPFLGKLLKQYLTSYYAREWGTLIG</entry><entry>223</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>QGIELDQIVKVMQNQKSKLFREIGYDMEEGFLSGKAFHQKVLDYPFFLTELSLMIEYGQV</entry><entry>239</entry></row><row><entry /><entry /><entry>QG++L  I+ +M  +KS L +E+  D+    L G+AFH KV  YPFF  ELSLMIEYG++</entry></row><row><entry>Sbjct:</entry><entry>224</entry><entry>QGLDLMTILDIMAIEKSSLMKELAEDIRMSLLEGQAFHIKVATYPFFKKELSLMIEYGEI</entry><entry>283</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>KAKLGTELDIYADEKWEDFFTKLARATQLIQPVIFIFVALIIVMIYAAMLLPMYQNM</entry><entry>296</entry></row><row><entry /><entry /><entry>K+KLG EL+IYA E WE FF++L + TQLIQP IF+ VA+ IVMIYAA+LLP+YQNM</entry></row><row><entry>Sbjct:</entry><entry>284</entry><entry>KSKLGAELEIYAQESWEQFFSQLYQVTQLIQPAIFLVVAVTIVMIYAAILLPIYQNM</entry><entry>340</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8493&gt; and protein &lt;SEQ ID 8494&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00412" num="00412"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 9</entry><entry /></row><row><entry>SRCFLG: 0</entry></row><row><entry>McG: Length of UR: 2</entry></row><row><entry>Peak Value of UR: 1.24</entry></row><row><entry>Net Charge of CR: 0</entry></row><row><entry>McG: Discrim Score: −8.94</entry></row><row><entry>GvH: Signal Score (−7.5): −4.08</entry></row><row><entry>Possible site: 31</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>Amino Acid Composition: calculated from 1</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 4</entry><entry>value: −14.65</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="21pt" align="left" /><colspec colname="6" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −14.65</entry><entry>Transmembrane</entry><entry>105-121 (95-126) </entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −13.53</entry><entry>Transmembrane</entry><entry>254-270 (246-277)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −8.55</entry><entry>Transmembrane</entry><entry>61-77 (57-84)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 5.09</entry><entry>14</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 3.43</entry><entry /></row><row><entry>icm1 HYPID: 7 CFP: 0.686</entry></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial membrane --- Certainty = 0.6859 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00012" num="00012"><img id="EMI-C00012" he="91.78mm" wi="118.62mm" file="US07939087-20110510-C00012.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00012" attachment-type="cdx" file="US07939087-20110510-C00012.CDX" /><attachment idref="CHEM-US-00012" attachment-type="mol" file="US07939087-20110510-C00012.MOL" /></attachments></chemistry>

SEQ ID 8494 (GBS49) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 11</figref> (lane 5; MW 15 kDa). It was also was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 15</figref> (lane 5; MW 60 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 118

A DNA sequence (GBSx0123) was identified in <i>S. agalactiae </i>&lt;SEQ ID 397&gt; which encodes the amino acid sequence &lt;SEQ ID 398&gt;. This protein is predicted to be ComYD or ComGD. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00413" num="00413"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="266pt" align="left" /><colspec colname="2" colwidth="175pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00414" num="00414"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA75315 GB: Y15043 homology to ComYD from <i>Streptcoccus gordonii</i>,</entry><entry /></row><row><entry>and ComGD from <i>Bacillus subtilis </i>[<i>Lactococcus lactis </i>subsp. <i>cremoris</i>]</entry></row><row><entry>Identities = 56/138 (40%), Positives = 92/138 (66%), Gaps = 2/138 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>12</entry><entry>KVKAFTLLECLVALVTITGALLVYQGLTKLLAQQIVVMSSSSQSEWVLLTQQLNAEFEGA</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>K++AFTLLECLVAL+ I+G++LV  GLT+++ +Q+ +  + S+ +W +  +Q+ +E  GA</entry></row><row><entry>Sbjct:</entry><entry>13</entry><entry>KIRAFTLLECLVALLAISGSVLVISGLTRMIEEQMKISQNDSRKDWQIFCEQMRSELSGA</entry><entry>72</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>HLEYLRQNKLYLRKQDKIVTFGKSNKDDFRKTGYDGRGYQPMVYGLDNCQMSQTKSMVKL</entry><entry>131</entry></row><row><entry /><entry /><entry> L+ + QN LY+ K DK + FG    DDFRK+   G+GYQPM+Y L   ++   ++++K+</entry></row><row><entry>Sbjct:</entry><entry>73</entry><entry>KLDNVNQNFLYVTK-DKKLRFGLVG-DDFRKSDDKGQGYQPMLYDLKGAKIQAEENLIKI</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>VFYFKDGLKRTFYYDFKE</entry><entry>149</entry></row><row><entry /><entry /><entry>   F +G +R F Y F +</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>TIDFDNGGERVFIYRFTD</entry><entry>148</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 399&gt; which encodes the amino acid sequence &lt;SEQ ID 400&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00415" num="00415"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="266pt" align="left" /><colspec colname="2" colwidth="175pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00416" num="00416"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA75315 GB: Y15043 homology to ComYD from <i>Streptcoccus gordonii</i>,</entry><entry /></row><row><entry>and ComGD from <i>Bacillus subtilis </i>[<i>Lactococcus lactis </i>subsp. <i>cremoris</i>]</entry></row><row><entry>Identities = 65/137 (47%), Positives = 84/137 (60%), Gaps = 2/137 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>IKAFTLLEALIALLVISGSLLVYQGLTRTLLKHSHYLARHDQDNWLLFSHQLREELSGAR</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>I+AFTLLE L+ALL ISGS+LV  GLTR + +         + +W +F  Q+R ELSGA+</entry></row><row><entry>Sbjct:</entry><entry>14</entry><entry>IRAFTLLECLVALLAISGSVLVISGLTRMIEEQMKISQNDSRKDWQIFCEQMRSELSGAK</entry><entry>73</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>FYKVADNKLYVEKGKKVLAFGQFKSHDFRKSASNGKGYQPMLFGISRSHIHIEQSQICIT</entry><entry>127</entry></row><row><entry /><entry /><entry>   V  N LYV K KK L FG     DFRKS   G+GYQPML+ +  + I  E++ I IT</entry></row><row><entry>Sbjct:</entry><entry>74</entry><entry>LDNVNQNFLYVTKDKK-LRFG-LVGDDFRKSDDKGQGYQPMLYDLKGAKIQAEENLIKIT</entry><entry>131</entry></row><row><entry /></row><row><entry>Query:</entry><entry>128</entry><entry>LKWKSGLERTFYYAFQD</entry><entry>144</entry></row><row><entry /><entry /><entry>+ + +G ER F Y F D</entry></row><row><entry>Sbjct:</entry><entry>132</entry><entry>IDFDNGGERVFIYRFTD</entry><entry>148</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00417" num="00417"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 58/137 (42%), Positives = 88/137 (63%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>VKAFTLLECLVALVTITGALLVYQGLTKLLAQQIVVMSSSSQSEWVLLTQQLNAEFEGAH</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>+KAFTLLE L+AL+ I+G+LLVYQGLT+ L +    ++   Q  W+L + QL  E  GA</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>IKAFTLLEALIALLVISGSLLVYQGLTRTLLKHSHYLARHDQDNWLLFSHQLREELSGAR</entry><entry>67</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>LEYLRQNKLYLRKQDKIVTFGKSNKDDFRKTGYDGRGYQPMVYGLDNCQMSQTKSMVKLV</entry><entry>132</entry></row><row><entry /><entry /><entry>   +  NKLY+ K  K++ FG+    DFRK+  +G+GYQPM++G+    +   +S + +</entry></row><row><entry>Sbjct:</entry><entry>68</entry><entry>FYKVADNKLYVEKGKKVLAFGQFKSHDFRKSASNGKGYQPMLFGISRSHIHIEQSQICIT</entry><entry>127</entry></row><row><entry /></row><row><entry>Query:</entry><entry>133</entry><entry>FYFKDGLKRTFYYDFKE</entry><entry>149</entry></row><row><entry /><entry /><entry>  +K GL+RTFYY F++</entry></row><row><entry>Sbjct:</entry><entry>128</entry><entry>LKWKSGLERTFYYAFQD</entry><entry>144</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8495&gt; and protein &lt;SEQ ID 8496&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00418" num="00418"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: 4.86</entry></row><row><entry>GvH: Signal Score (−7.5): −0.22</entry></row><row><entry>Possible site: 55</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 0</entry><entry>value: 12.47</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 12.47</entry><entry>127</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −2.99</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial outside --- Certainty = 0.3000 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00013" num="00013"><img id="EMI-C00013" he="69.43mm" wi="118.62mm" file="US07939087-20110510-C00013.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00013" attachment-type="cdx" file="US07939087-20110510-C00013.CDX" /><attachment idref="CHEM-US-00013" attachment-type="mol" file="US07939087-20110510-C00013.MOL" /></attachments></chemistry>

SEQ ID 398 (GBS6) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 1</figref> (lane 2; MW 40 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 2</figref> (lane 2; MW 15 kDa). The GBS6-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 189</figref>, lane 2) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 260</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 119

A DNA sequence (GBSx0124) was identified in <i>S. agalactiae </i>&lt;SEQ ID 401&gt; which encodes the amino acid sequence &lt;SEQ ID 402&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00419" num="00419"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3831(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00420" num="00420"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC00317 GB: AF008220 YtxK [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 106/329 (32%), Positives = 176/329 (53%), Gaps = 17/329 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNFEKIETAYELILENIQTIENQLKTHIYDALIEQNSYYLGSSCDLDMVVVNNQKLRQLD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M  + +   YEL+ E    I+N+L+    +AL E    Y     D  + +  +QK +QL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MQKDHVGAVYELLNEAAIMIKNELQISYIEALAEAGEMYFLEKTD-QLKLPADQKTKQLQ</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LSQE---------EW-RRTFQFIFIKSAQTEQLQANHQFTPDSIGFILLFLLEE-LTSQE</entry><entry>109</entry></row><row><entry /><entry /><entry>   E         EW R+ FQ   +K  + +    N Q TPD+IG  + +L+ + +  ++</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>ALLEKAEFGTYEHEWVRKAFQLAVLKGMK-DISHPNRQMTPDTIGLFISYLVNKFMADKK</entry><entry>118</entry></row><row><entry /></row><row><entry>Query:</entry><entry>110</entry><entry>TVDVLEIGSGTGNLAQTLLNN-SSKELNYMGIEVDDLLIDLSASIAEIIGSSAQFIQEDA</entry><entry>168</entry></row><row><entry /><entry /><entry> + +L+   GTGNL  T+LN  S K  N  GIE+DD+L+ ++ + A ++    +   +D+</entry></row><row><entry>Sbjct:</entry><entry>119</entry><entry>ELTILDPALGTGNLLFTVLNQLSEKTANSFGIEIDDVLLKIAYAQANLLKKELELFHQDS</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>169</entry><entry>VRPQILKESDVIISDLPVGYYPNDGIAKRYAVSSSKEHTYAHHLLMEQSLKYLKKDGIAI</entry><entry>228</entry></row><row><entry /><entry /><entry>+ P  +   D +I DLPVGYYPND  A+ + + + + H++AHHL +EQS+K+ K  G</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>LEPLFIDPVDTVICDLPVGYYPNDEGAEAFELKADEGHSFAHHLFIEQSVKHTKPGGYLF</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>229</entry><entry>FLAPENLLTSPQSDLLKEWLKGYADVIAVLTLPETIFGSRQNAKSIFVLKKQAEQKP---</entry><entry>285</entry></row><row><entry /><entry /><entry>F+ P +L  S QS  LK++ K    + A+L LP++IF    +AKSI VL+KQ E</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>FMIPNHLFESSQSGKLKQFFKDKVHINALLQLPKSIFKDEAHAKSILVLQKQGENTKAPG</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>286</entry><entry>ETFVYPLTDLQNRENMANFIENFQKWSRE</entry><entry>314</entry></row><row><entry /><entry /><entry>+  +  L    N++ M + +  F +W ++</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>QILLANLPSFSNQKAMLDMMAQFDEWFKK</entry><entry>327</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 403&gt; which encodes the amino acid sequence &lt;SEQ ID 404&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00421" num="00421"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00422" num="00422"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 223/315 (70%), Positives = 270/315 (84%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNFEKIETAYELILENIQTIENQLKTHIYDALIEQNSYYLGSSCDLDMVVVNNQKLRQLD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M FEKIE AY+L+LEN Q IEN LKTHIYDA++EQNS+YLG+      V  N+ KL+ L</entry></row><row><entry>Sbjct:</entry><entry>16</entry><entry>MTFEKIEEAYQLLLENCQLIENDLKTHIYDAIVEQNSFYLGAEGASPQVAQNSDKLKALC</entry><entry>75</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LSQEEWRRTFQFIFIKSAQTEQLQANHQFTPDSIGFILLFLLEELTSQETVDVLEIGSGT</entry><entry>120</entry></row><row><entry /><entry /><entry>L++EEWR+ +QF+FIK+AQTEQLQANHQFTPD+IGFILL+LLE+L+ +++++VLEIGSGT</entry></row><row><entry>Sbjct:</entry><entry>76</entry><entry>LTKEEWRKAYQFLFIKAAQTEQLQANHQFTPDAIGFILLYLLEQLSDKDSLEVLEIGSGT</entry><entry>135</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GNLAQTLLNNSSKELNYMGIEVDDLLIDLSASIAEIIGSSAQFIQEDAVRPQILKESDVI</entry><entry>180</entry></row><row><entry /><entry /><entry>GNLAQTLLNN+SK L+Y+GIE+DDLLIDLSASIAEI+ SSA FIQEDAVRPQ+LKESD++</entry></row><row><entry>Sbjct:</entry><entry>136</entry><entry>GNLAQTLLNNTSKSLDYVGIELDDLLIDLSASIAEIMDSSAHFIQEDAVRPQLLKESDIV</entry><entry>195</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>ISDLPVGYYPNDGIAKRYAVSSSKEHTYAHHLLMEQSLKYLKKDGIAIFLAPENLLTSPQ</entry><entry>240</entry></row><row><entry /><entry /><entry>ISDLPVGYYPND IAKRY V+SS +HTYAHHLLMEQSLKYLKKDG AIFLAP NLLTSPQ</entry></row><row><entry>Sbjct:</entry><entry>196</entry><entry>ISDLPVGYYPNDDIAKRYKVASSDKHTYAHHLLMEQSLKYLKKDGFAIFLAPVNLLTSPQ</entry><entry>255</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>SDLLKEWLKGYADVIAVLTLPETIFGSRQNAKSIFVLKKQAEQKPETFVYPLTDLQNREN</entry><entry>300</entry></row><row><entry /><entry /><entry>S LLK+WLK YA V+ ++TLP++IFG   NAKSI VL+KQ +   ETFVYP+ DL+  EN</entry></row><row><entry>Sbjct:</entry><entry>256</entry><entry>SQLLKQWLKDYAQVVTLITLPDSIFGHPSNAKSIIVLQKQTDHPMETFVYPIRDLKLAEN</entry><entry>315</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>MANFIENFQKWSREN</entry><entry>315</entry></row><row><entry /><entry /><entry>+ +F+ENF+KW   N</entry></row><row><entry>Sbjct:</entry><entry>316</entry><entry>IHDFMENFKKWKLSN</entry><entry>330</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 120

A DNA sequence (GBSx0125) was identified in <i>S. agalactiae </i>&lt;SEQ ID 405&gt; which encodes the amino acid sequence &lt;SEQ ID 406&gt;. This protein is predicted to be acetate kinase (ackA-1). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00423" num="00423"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2384(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00424" num="00424"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC36857 GB: L17320 acetate kinase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 223/395 (56%), Positives = 293/395 (73%), Gaps = 3/395 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKTIAINAGSSSLKWQLYEMPEEKVVAKGIIERIGLKDSISTVKFDDKKDEQILDIVDH</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MSK IAINAGSSSLK+QL+EMP E V+ KG++ERIG+ DS+ T+  + +K+ ++ DI DH</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TQAVKILLEDLTKHGIIKDFNEITGVGHRVVAGGEYFKESALVDDKVVEQVEELSALAPL</entry><entry>120</entry></row><row><entry /><entry /><entry>  AVK+LL  LT+ GIIKD NEI G+GHRVV GGE F +S L+ D+ ++++E++S LAPL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HNPAAAAGIRAFREILPDITSVCVFDTAFHTTMQPHTYLYPIPQKYYTDYKVRKYGAHGT</entry><entry>180</entry></row><row><entry /><entry /><entry>HNPA   GI+AF+E+LP++ +V VFDTAFH TM   +YLY +P +YY  + +RKYG HGT</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SHQYVAQEAAKQLGRPLEELKLITAHVGNGVSITANYHGQSIDTSMGFTPLAGPMMGTRS</entry><entry>240</entry></row><row><entry /><entry /><entry>SH+YV + AA+ LGRPL++L+LI+ H+GNG SI A   G+SIDTSMGFTPLAG  MGTRS</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDIDPAIIPYLVANDPELEDAAAVVNMLNKQSGLLGVSGTSSDMRDIEAGLQSKDPNAVL</entry><entry>300</entry></row><row><entry /><entry /><entry>G+IDPA+IPY++    +  D   V+N LNK+SGLLG+SG SSD+RDI    +  +  A</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GNIDPALIPYIMEKTGQTAD--EVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAET</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>AYNVFIDRIKKFIGQYLAVLNGADAIIFTAGMGENAPLMRQDVIAGLSWFGIELDPE-KN</entry><entry>359</entry></row><row><entry /><entry /><entry>A  VF  RI K+IG Y A ++G DAIIFTAG+GEN+  +R+ V+ GL + G+  DP   N</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNN</entry><entry>358</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>VFGYFGDITKPDSKVKVLVIPTDEELMIARDVERL</entry><entry>394</entry></row><row><entry /><entry /><entry>V G    I+ P S VKV++IPTDEE+MIARDV RL</entry></row><row><entry>Sbjct:</entry><entry>359</entry><entry>VRGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL</entry><entry>393</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 407&gt; which encodes the amino acid sequence &lt;SEQ ID 408&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00425" num="00425"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −0.22</entry><entry>Transmembrane</entry><entry>63-79 (63-79)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.1086 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00426" num="00426"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC36857 GB: L17320 acetate kinase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 218/395 (55%), Positives = 293/395 (73%), Gaps = 3/395 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKTIAINAGSSSLKWQLYQMPEEAVLAQGIIERIGLKDSISTVKYDGKKEEQILDIHDH</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MSK IAINAGSSSLK+QL++MP E VL +G++ERIG+ DS+ T+  +G+K  ++ DI DH</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TEAVKILLNDLIHFGIIAAYDEITGVGHRVVAGGELFKESVVVNDKVLEQIEELSVLAPL</entry><entry>120</entry></row><row><entry /><entry /><entry>  AVK+LLN L  FGII   +EI G+GHRVV GGE F +SV++ D+ +++IE++S LAPL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HNPGAAAGIRAFRDILPDITSVCVFDTSFHTSMAKHTYLYPIPQKYYTDYKVRKYGAHGT</entry><entry>180</entry></row><row><entry /><entry /><entry>HNP    GI+AF+++LP++ +V VFDT+FH +M + +YLY +P +YY  + +RKYG HGT</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SHKYVAQEAAKMLGRPLEELKLITAHIGNGVSITANYHGKSVDTSMGFTPLAGPMMGTRS</entry><entry>240</entry></row><row><entry /><entry /><entry>SHKYV + AA++LGRPL++L+LI+ H+GNG SI A   GKS+DTSMGFTPLAG  MGTRS</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDIDPAIIPYLIEQDPELKDAADVVNMLNKKSGLSGVSGISSDMRDIEAGLQEDNPDAVL</entry><entry>300</entry></row><row><entry /><entry /><entry>G+IDPA+IPY++E+  +  D  +V+N LNKKSGL G+SG SSD+RDI    +E N  A</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GNIDPALIPYIMEKTGQTAD--EVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAET</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>AYNIFIDRIKKCIGQYFAVLNGADALVFTAGMGENAPLMRQDVIGGLTWFGMDIDPE-KN</entry><entry>359</entry></row><row><entry /><entry /><entry>A  +F  RI K IG Y A ++G DA++FTAG+GEN+  +R+ V+ GL + G+  DP   N</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNN</entry><entry>358</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>VFGYRGDISTPESKVKVLVISTDEELCIARDVERL</entry><entry>394</entry></row><row><entry /><entry /><entry>V G    IS P S VKV++I TDEE+ IARDV RL</entry></row><row><entry>Sbjct:</entry><entry>359</entry><entry>VRGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL</entry><entry>393</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00427" num="00427"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 332/395 (84%), Positives = 365/395 (92%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSKTIAINAGSSSLKWQLYEMPEEKVVAKGIIERIGLKDSISTVKFDDKKDEQILDIVDH</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MSKTIAINAGSSSLKWQLY+MPEE V+A+GIIERIGLKDSISTVK+D KK+EQILDI DH</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKTIAINAGSSSLKWQLYQMPEEAVLAQGIIERIGLKDSISTVKYDGKKEEQILDIHDH</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TQAVKILLEDLTKHGIIKDFNEITGVGHRVVAGGEYFKESALVDDKVVEQVEELSALAPL</entry><entry>120</entry></row><row><entry /><entry /><entry>T+AVKILL DL   GII  ++EITGVGHRVVAGGE FKES +V+DKV+EQ+EELS LAPL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TEAVKILLNDLIHFGIIAAYDEITGVGHRVVAGGELFKESVVVNDKVLEQIEELSVLAPL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HNPAAAAGIRAFREILPDITSVCVFDTAFHTTMQPHTYLYPIPQKYYTDYKVRKYGAHGT</entry><entry>180</entry></row><row><entry /><entry /><entry>HNP AAAGIRAFR+ILPDITSVCVFDT+FHT+M  HTYLYPIPQKYYTDYKVRKYGAHGT</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>HNPGAAAGIRAFRDILPDITSVCVFDTSFHTSMAKHTYLYPIPQKYYTDYKVRKYGAHGT</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SHQYVAQEAAKQLGRPLEELKLITAHVGNGVSITANYHGQSIDTSMGFTPLAGPMMGTRS</entry><entry>240</entry></row><row><entry /><entry /><entry>SH+YVAQEAAK LGRPLEELKLITAH+GNGVSITANYHG+S+DTSMGFTPLAGPMMGTRS</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SHKYVAQEAAKMLGRPLEELKLITAHIGNGVSITANYHGKSVDTSMGFTPLAGPMMGTRS</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>GDIDPAIIPYLVANDPELEDAAAVVNMLNKQSGLLGVSGTSSDMRDIEAGLQSKDPNAVL</entry><entry>300</entry></row><row><entry /><entry /><entry>GDIDPAIIPYL+  DPEL+DAA VVNMLNK+SGL GVSG SSDMRDIEAGLQ  +P+AVL</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GDIDPAIIPYLIEQDPELKDAADVVNMLNKKSGLSGVSGISSDMRDIEAGLQEDNPDAVL</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>AYNVFIDRIKKFIGQYLAVLNGADAIIFTAGMGENAPLMRQDVIAGLSWFGIELDPEKNV</entry><entry>360</entry></row><row><entry /><entry /><entry>AYN+FIDRIKK IGQY AVLNGADA++FTAGMGENAPLMRQDVI GL+WFG+++DPEKNV</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>AYNIFIDRIKKCIGQYFAVLNGADALVFTAGMGENAPLMRQDVIGGLTWFGMDIDPEKNV</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>FGYFGDITKPDSKVKVLVIPTDEELMIARDVERLK</entry><entry>395</entry></row><row><entry /><entry /><entry>FGY GDI+ P+SKVKVLVI TDEEL IARDVERLK</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>FGYRGDISTPESKVKVLVISTDEELCIARDVERLK</entry><entry>395</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 121

A DNA sequence (GBSx0126) was identified in <i>S. agalactiae </i>&lt;SEQ ID 409&gt; which encodes the amino acid sequence &lt;SEQ ID 410&gt;. This protein is predicted to be repressor protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00428" num="00428"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00429" num="00429"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB49550 GB: AJ248284 repressor protein, putative [<i>Pyrococcus</i></entry><entry /></row><row><entry><i>abyssi</i>]</entry></row><row><entry>Identities = 39/64 (60%), Positives = 49/64 (75%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKNSLQKLRKSRKLSQAELAVALGVTRQTIISLEKEKYTASLELAFKIARYFDKQIEEVF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKN L++ R+   L+Q ELA  LGVTRQTII++EK KY  SL LAFKIAR+F  +IE++F</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKNRLREFREKYGLTQEELARILGVTRQTIIAIEKGKYDPSLRLAFKIARFFGVRIEDIF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IYTE</entry><entry>64</entry></row><row><entry /><entry /><entry>IY E</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>IYEE</entry><entry>64</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 411&gt; which encodes the amino acid sequence &lt;SEQ ID 412&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00430" num="00430"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4344(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00431" num="00431"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 29/66 (43%), Positives = 44/66 (65%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKNSLQKLRKSRKLSQAELAVALGVTRQTIISLEKEKYTASLELAFKIARYFDKQIEEVF</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+KN L++LR    ++Q E+A   GV+RQTI  +E+ +YT S+ +A KIA+ F + +EEVF</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>LKNRLKELRARDGINQTEMAKLAGVSRQTISLIERNEYTPSVIIAMKIAKVFQEPVEEVF</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IYTESE</entry><entry>66</entry></row><row><entry /><entry /><entry>   E E</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>RLVEVE</entry><entry>75</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 122

A DNA sequence (GBSx0127) was identified in <i>S. agalactiae </i>&lt;SEQ ID 413&gt; which encodes the amino acid sequence &lt;SEQ ID 414&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00432" num="00432"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.97</entry><entry>Transmembrane</entry><entry>  45-61 (41-66)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.65</entry><entry>Transmembrane</entry><entry>  14-30 (11-37)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.80</entry><entry>Transmembrane</entry><entry>123-139 (118-145)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.24</entry><entry>Transmembrane</entry><entry>177-193 (177-194)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.85</entry><entry>Transmembrane</entry><entry>  81-97 (81-97)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4588(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9491&gt; which encodes amino acid sequence &lt;SEQ ID 9492&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00433" num="00433"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAA11325 GB: D78257 ORF8 [<i>Enterococcus faecalis</i>]</entry><entry /></row><row><entry>Identities = 48/120 (40%), Positives = 69/120 (57%), Gaps = 5/120 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>104</entry><entry>MQGVKDTANQTVIMELTKQLPLALMLIFAIIGAPIMEEIIFRYIIPKELFAKHQKWGFVI</entry><entry>163</entry><entry /></row><row><entry /><entry /><entry>MQG   TAN + +++L   +   L+++   I APIMEEI+FR  I   L   +     +I</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MQGHTTTANDSTLIKLFSGVSPVLVVLLLGIAAPIMEEIVFRGGIIGYLVENNALLAILI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>164</entry><entry>GTLAFALIHSPSDIGSFIIYAGMGAILSFVYYKTEHLEYSIMIHFINN-----ALAYSVL</entry><entry>218</entry></row><row><entry /><entry /><entry> +  F +IH P++  SF +Y  MG ILS  YYKT+ L  SI IHF+NN     A+AY ++</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>SSFLFGIIHGPTNFISFGMYFFMGIILSVSYYKTKDLRVSISIHFLNNLFPAIAIAYGLI</entry><entry>120</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 415&gt; which encodes the amino acid sequence &lt;SEQ ID 416&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00434" num="00434"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.41</entry><entry>Transmembrane</entry><entry>  12-28 (1-30)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.98</entry><entry>Transmembrane</entry><entry>  41-57 (33-64)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.33</entry><entry>Transmembrane</entry><entry>128-144 (121-151)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.96</entry><entry>Transmembrane</entry><entry>  83-99 (76-103)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry>208-224 (207-230)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.13</entry><entry>Transmembrane</entry><entry>182-198 (182-199)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5564(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00435" num="00435"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAA11325 GB: D78257 ORF8 [<i>Enterococcus faecalis</i>]</entry><entry /></row><row><entry>Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 8/120 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>105</entry><entry>GQQVSANDAAIHTLARLIKGGFPLYTALFVLVIAFIAPIMEELVFRGFPMIDLFKGKSLK</entry><entry>164</entry><entry /></row><row><entry /><entry /><entry>G   +AND+   TL +L  G  P+   L VL++   APIMEE+VFRG  +  L +  +L</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>GHTTTANDS---TLIKLFSGVSPV---LVVLLLGIAAPIMEEIVFRGGIIGYLVENNAL-</entry><entry>55</entry></row><row><entry /></row><row><entry>Query:</entry><entry>165</entry><entry>VAGLVTSLVFALPHA-TNSVEFIMYSCMGIFLFVAYQRRGNLKDAILLHIFNNLIEVILL</entry><entry>223</entry></row><row><entry /><entry /><entry>+A L++S +F + H  TN + F MY  MGI L V+Y +  +L+ +I +H  NNL   I +</entry></row><row><entry>Sbjct:</entry><entry>56</entry><entry>LAILISSFLFGIIHGPTNFISFGMYFFMGIILSVSYYKTKDLRVSISIHFLNNLFPAIAI</entry><entry>115</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00436" num="00436"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 72/229 (31%), Positives = 114/229 (49%), Gaps = 24/229 (10%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>KGKILALLIAFLVINQLV-PILAVWLLKNHYQTPFTSILLIGL-------ELLIIALFLY</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>KG I  L IA L+I  +V  +L + LL+  +  P      IG+        +LI+   LY</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KGFINYLKIAVLIILAMVFNVLPMILLQKQHDIPMVLNWGIGIFYLVIVGSVLIVLWGLY</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>YAKVKQIIRWKALLTRKALVT---ILLGWLSLRVPQIIGYLIMTM-QGVKDTANQTVIME</entry><entry>118</entry></row><row><entry /><entry /><entry> AK    I+ + +     LV    + L WL +RV  I+G L+  +  G + +AN   I</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>QAKQDTFIKQQKM----RLVDWGYLALFWLIIRVIAIVGTLVNQLWSGQQVSANDAAIHT</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>LTKQL----PLALMLIFAIIG--APIMEEIIFRYIIPKELF-AKHQKWGFVIGTLAFALI</entry><entry>171</entry></row><row><entry /><entry /><entry>L + +    PL   L   +I   APIMEE++FR     +LF  K  K   ++ +L FAL</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>LARLIKGGFPLYTALFVLVIAFIAPIMEELVFRGFPMIDLFKGKSLKVAGLVTSLVFALP</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>172</entry><entry>HSPSDIGSFIIYAGMGAILSFVYYKTEHLEYSIMIHFINNALAYSVLIS</entry><entry>220</entry></row><row><entry /><entry /><entry>H+ + +  FI+Y+ MG  L   Y +  +L+ +I++H  NN +   +L+S</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>HATNSV-EFIMYSCMGIFLFVAYQRRGNLKDAILLHIFNNLIEVILLMS</entry><entry>225</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 123

A DNA sequence (GBSx0128) was identified in <i>S. agalactiae </i>&lt;SEQ ID 417&gt; which encodes the amino acid sequence &lt;SEQ ID 418&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00437" num="00437"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0826(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00438" num="00438"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC06504 GB: AE000676 pyrroline carboxylate reductase [<i>Aquifex</i></entry><entry /></row><row><entry><i>aeolicus</i>]</entry></row><row><entry>Identities = 97/259 (37%), Positives = 159/259 (60%), Gaps = 4/259 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKIGIIGVGKM--ASAIIQGLKQTQHDIIISGSCLERSKEIAERLDVTYAESHQSLINQA</entry><entry>58</entry><entry /></row><row><entry /><entry /><entry>M++GI+G G M  A A+    K  + +II++    E+ + +A  + + +A   + L + +</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>MRVGIVGFGNMGQAFALCFSKKLGKENIIVTDKVQEK-RNLATEMGIAFASDVKFLADNS</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>59</entry><entry>DIIMLGIKPQLFEKVLLPLDITKPII-SMAAGISLARLSQLTRSDLPLIRIMPNINAQIL</entry><entry>117</entry></row><row><entry /><entry /><entry>D++++ +KP+  ++VL  L   K II S+ AG+S+ ++ ++   D  ++R+MPN+N  +</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>DVVLVAVKPKDSQEVLQKLKDYKGIILSIMAGVSIEKMEKILGKDKKIVRVMPNVNVAVG</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>QSCTAICYNNHVSDELRQLAKEITDSFGSSFDIAETNFDTFTALAGSSPAYIYLFIEALA</entry><entry>177</entry></row><row><entry /><entry /><entry>    AI  N ++S+E R   +E+  S G+ + I E  FD FTALAGS PA+++ FI+ALA</entry></row><row><entry>Sbjct:</entry><entry>127</entry><entry>SGVMAITDNGNLSEEERSKVEELLLSCGTLYRIEERLFDAFTALAGSGPAFVFSFIDALA</entry><entry>186</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>KAGVKYGFPKEQALSIVGQTVLASSQNLLQGQNSTSDLIDNICSPGGTTIAGLLDLEKNG</entry><entry>237</entry></row><row><entry /><entry /><entry> AGV  GF  EQAL I   TV+ S++ L + Q + ++LI  + SPGGTTI G+  LE+ G</entry></row><row><entry>Sbjct:</entry><entry>187</entry><entry>LAGVHQGFSYEQALRIALDTVMGSAKLLKEFQVNPNELIAKVTSPGGTTIEGIKYLEEKG</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>LTHSVISAIDATIEKAKKL</entry><entry>256</entry></row><row><entry /><entry /><entry>   +V+  I+ T +KAKKL</entry></row><row><entry>Sbjct:</entry><entry>247</entry><entry>FKGTVMECINRTSQKAKKL</entry><entry>265</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 419&gt; which encodes the amino acid sequence &lt;SEQ ID 420&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00439" num="00439"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1043(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00440" num="00440"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 180/256 (70%), Positives = 208/256 (80%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKIGIIGVGKMASAIIQGLKQTQHDIIISGSCLERSKEIAERLDVTYAESHQSLINQADI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MKIGIIGVGKMASAII+GLKQT H++IISGS LERSKEIAE+L + YA SHQ LI+Q D+</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKIGIIGVGKMASAIIKGLKQTPHELIISGSSLERSKEIAEQLALPYAMSHQDLIDQVDL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IMLGIKPQLFEKVLLPLDITKPIISMAAGISLARLSQLTRSDLPLIRIMPNINAQILQSC</entry><entry>120</entry></row><row><entry /><entry /><entry>++LGIKPQLFE VL PL   +PIISMAAGISL RL+     DLPL+RIMPN+NAQILQS</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VILGIKPQLFETVLKPLHFKQPIISMAAGISLQRLATFVGQDLPLLRIMPNMNAQILQSS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TAICYNNHVSDELRQLAKEITDSFGSSFDIAETNFDTFTALAGSSPAYIYLFIEALAKAG</entry><entry>180</entry></row><row><entry /><entry /><entry>TA+  N  VS EL+   +++TDSFGS+FDI+E +FDTFTALAGSSPAYIYLFIEALAKAG</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TALTGNALVSQELQARVRDLTDSFGSTFDISEKDFDTFTALAGSSPAYIYLFIEALAKAG</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>VKYGFPKEQALSIVGQTVLASSQNLLQGQNSTSDLIDNICSPGGTTIAGLLDLEKNGLTH</entry><entry>240</entry></row><row><entry /><entry /><entry>VK G PK +AL IV QTVLAS+ NL     S  D ID ICSPGGTTIAGL++LE+ GLT</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VKNGIPKAKALEIVTQTVLASASNLKTSSQSPHDFIDAICSPGGTTIAGLMELERLGLTA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>SVISAIDATIEKAKKL</entry><entry>256</entry></row><row><entry /><entry /><entry>+V SAID TI+KAK L</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>TVSSAIDKTIDKAKSL</entry><entry>256</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 124

A DNA sequence (GBSx0129) was identified in <i>S. agalactiae </i>&lt;SEQ ID 421&gt; which encodes the amino acid sequence &lt;SEQ ID 422&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00441" num="00441"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3405(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00442" num="00442"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA56994 GB:X81089 glutamyl-aminopeptidase [<i>Lactococcus lactis</i>]</entry><entry /></row><row><entry>Identities = 219/354 (61%), Positives = 273/354 (76%), Gaps = 1/354 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>DLFNKIKTVTELDGIAGYEHNIRNFLRQEITPLVDQVETDGLGGIFGVKNTHETNAPKVM</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>+LF+K+K +TE+   +G+E  +R++L+  +  L  Q E DGLGGIF  K +   NAP++M</entry><entry /></row><row><entry>Sbjct:</entry><entry>2</entry><entry>ELFDKVKALTEIQATSGFEGPVRDYLKARMVELGYQPEFDGLGGIFVTKASKVENAPRIM</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>VAAHMDEVGFMVSHIQPDGTFRVLEVGGWNPLVVSSQRFTLYTRSGDAIPVISGSVPPHF</entry><entry>122</entry></row><row><entry /><entry /><entry>VAAHMDEVGFMVS I+ DGTFRV+ +GGWNPLVVS QRFTL+TR+G  IPV++G +PPH</entry><entry /></row><row><entry>Sbjct:</entry><entry>62</entry><entry>VAAHMDEVGFMVSSIKADGTFRVVPLGGWNPLVVSGQRFTLFTRTGKKIPVVTGGLPPHL</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>LRGQSGGTTLPKISDIVFDGGFTDKNEAESFGIAPGDIIVPKSETILTANQKHIMSKAWD</entry><entry>182</entry></row><row><entry /><entry /><entry>LRG      +P ISDI+FDG F +  KA  FGIA GD+I+P++ETIL+AN K+I+SKAWD</entry><entry /></row><row><entry>Sbjct:</entry><entry>122</entry><entry>LRGTGVTPQIPAISDIIFDGAFENAAEAAEFGIAQGDLIIPETETILSANGKNIISKAWD</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>NRYGVLMVTELLKSLKDQSLSNTLIAGANVQEEVGLRGAHVSTTKFNPDIFLAVDCSPAG</entry><entry>242</entry></row><row><entry /><entry /><entry>NRYG LM+ ELL+ L D+ L  TLI GANVQEEVGLRGA VSTTKFNPD+F AVDCSPA</entry><entry /></row><row><entry>Sbjct:</entry><entry>182</entry><entry>NRYGCLMILELLEFLADKELPVTLIIGANVQEEVGLRGAKVSTTKFNPDLFFAVDCSPAS</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>DIYG-EQGKIGEGTLIRFYDPGHIMLKDMRDFLLTTAEEAGIKYQYYAANGGTDAGAAHL</entry><entry>301</entry></row><row><entry /><entry /><entry>D +G + G++GEGT +RF+DPGHIML  M++FLL TA  A +K Q Y A GGTDAGAAHL</entry><entry /></row><row><entry>Sbjct:</entry><entry>242</entry><entry>DTFGDDNGRLGEGTTLRFFDPGHIMLPGMKNFLLDTANHAKVKTQVYMAKGGTDAGAAHL</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>KNSGIPSTTIGVCARYIHSHQTLYAMDDFLQAQAYLQAIVNKLDRSTVDIIKGY</entry><entry>355</entry></row><row><entry /><entry /><entry> N G+PSTTIGV ARYIHSHQT++ +DDFLQAQ +L+AI+  L+   V  IK Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>302</entry><entry>ANGGVPSTTIGVVARYIHSHQTIFNIDDFLQAQTFLRAIITSLNTEKVAEIKNY</entry><entry>355</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 423&gt; which encodes the amino acid sequence &lt;SEQ ID 424&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00443" num="00443"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2747(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00444" num="00444"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 276/355 (77%), Positives = 322/355 (89%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSDLFNKIKTVTELDGIAGYEHNIRNFLRQEITPLVDQVETDGLGGIFGVKNTHETNAPK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+DLF+KIK VTELDGIAGYEH++R++LR +ITPLVD+VETDGLGGIFG++++    AP+</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTDLFSKIKEVTELDGIAGYEHSVRDYLRTKITPLVDRVETDGLGGIFGIRDSKAEKAPR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VMVAAHMDEVGFMVSHIQPDGTFRVLEVGGWNPLVVSSQRFTLYTRSGDAIPVISGSVPP</entry><entry>120</entry></row><row><entry /><entry /><entry>++VAAHMDEVGFMVS I+ DGT RV+ +GGWNPLVVSSQRFTLYTR+G  IP+ISGSVPP</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ILVAAHMDEVGFMVSDIKVDGTLRVVGIGGWNPLVVSSQRFTLYTRTGQVIPLISGSVPP</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>HFLRGQSGGTTLPKISDIVFDGGFTDKNEAESFGIAPGDIIVPKSETILTANQKHIMSKA</entry><entry>180</entry></row><row><entry /><entry /><entry>HFLRG +G  +LP I DIVFDGGFTDK EAE FGI PGDII+P+SETILTANQK+I+SKA</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>HFLRGANGSASLPHIEDIVFDGGFTDKAEAERFGITPGDIIIPQSETILTANQKNIISKA</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>WDNRYGVLMVTELLKSLKDQSLSNTLIAGANVQEEVGLRGAHVSTTKFNPDIFLAVDCSP</entry><entry>240</entry></row><row><entry /><entry /><entry>WDNRYGVLM+TE+L++LK Q L+NTLIAGANVQEEVGLRGAHVSTTKF+P++F AVDCSP</entry><entry /></row><row><entry>Sbjct:</entry><entry>181</entry><entry>WDNRYGVLMITEMLEALKGQDLNNTLIAGANVQEEVGLRGAHVSTTKFDPELFFAVDCSP</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>AGDIYGEQGKIGEGTLIRFYDPGHIMLKDMRDFLLTTAEEAGIKYQYYAANGGTDAGAAH</entry><entry>300</entry></row><row><entry /><entry /><entry>AGDIYG  G IG+GTL+RFYDPGH+MLKDMRDFLLTTAEEAG+ +QYY   GGTDAGAAH</entry><entry /></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AGDIYGNPGTIGDGTLLRFYDPGHVMLKDMRDFLLTTAEEAGVNFQYYCGKGGTDAGAAH</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>LKNSGIPSTTIGVCARYIHSHQTLYAMDDFLQAQAYLQAIVNKLDRSTVDIIKGY</entry><entry>355</entry></row><row><entry /><entry /><entry>L+N G+PSTTIGVCARYIHSHQTLYAMDDF++AQA+LQAI+ KLDRSTVD+IK Y</entry><entry /></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LQNGGVPSTTIGVCARYIHSHQTLYAMDDFVEAQAFLQAIIKKLDRSTVDLIKCY</entry><entry>355</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 125

A DNA sequence (GBSx0130) was identified in <i>S. agalactiae </i>&lt;SEQ ID 425&gt; which encodes the amino acid sequence &lt;SEQ ID 426&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00445" num="00445"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 26</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1672(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 126

A DNA sequence (GBSx0131) was identified in <i>S. agalactiae </i>&lt;SEQ ID 427&gt; which encodes the amino acid sequence &lt;SEQ ID 428&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00446" num="00446"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.28</entry><entry>Transmembrane</entry><entry>18-34 (17-34)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1914(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 429&gt; which encodes the amino acid sequence &lt;SEQ ID 430&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00447" num="00447"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.16</entry><entry>Transmembrane</entry><entry>12-28 (8-30)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3463(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00448" num="00448"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 30/91 (32%), Positives = 48/91 (51%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>MKNKKILFGTGLAGVGLLAAAGYTLTKKVTDYKRQQITQTLREFFSQMGDIQVFYFNEFE</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>M  KKI   +G+ G  L    G  +     D +R+Q+T+ LR FFS +G I+V Y N  +</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>MSKKKIGMISGIFGFSLAIGLGIVIKDYCQDRQRRQMTRDLRTFFSPLGQIEVLYINPCQ</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>SDIKMTSGGLVLEDGRIFEFIYRQGVLDYVE</entry><entry>103</entry></row><row><entry /><entry /><entry>      SGG+V+ +G+ ++F Y    + + E</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>VKQDYISGGVVMSNGKQYQFTYHSRQISFEE</entry><entry>94</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8497&gt; and protein &lt;SEQ ID 8498&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00449" num="00449"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop Possible site: −1 Crend: 4</entry><entry /></row><row><entry>SRCFLG: 0</entry></row><row><entry>McG: Length of UR: 21</entry></row><row><entry>     Peak Value of UR: 2.30</entry></row><row><entry>     Net Charge of CR: 3</entry></row><row><entry>McG: Discrim Score: 6.28</entry></row><row><entry>GvH: Signal Score (−7.5): −1.46</entry></row><row><entry>     Possible site: 19</entry></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry>Amino Acid Composition: calculated from 20</entry></row><row><entry>ALOM program count: 0 value: 22.60 threshold: 0.0</entry></row><row><entry>   PERIPHERAL Likelihood = 22.60 29</entry></row><row><entry>modified ALOM score: −5.02</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry>Rule gpo1</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 8498 (GBS214) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 40</figref> (lane 3; MW 13.9 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 46</figref> (lane 6; MW 39 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 127

A DNA sequence (GBSx0132) was identified in <i>S. agalactiae </i>&lt;SEQ ID 431&gt; which encodes the amino acid sequence &lt;SEQ ID 432&gt;. This protein is predicted to be thioredoxin H1 (trxA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00450" num="00450"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2350(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00451" num="00451"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB06972 GB:AP001518 thioredoxin H1 [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 47/90 (52%), Positives = 66/90 (73%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>14</entry><entry>IDSTKKVVFFFTADWCPDCQFIYPVMPSIEKDFSDFVFVRVNRDDYIELAQQWNIFGIPS</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>+ + + VVF F+ADWCPDC+ I P +P +E+ + ++ F  VNRDD+IEL Q+ +IFGIPS</entry><entry /></row><row><entry>Sbjct:</entry><entry>13</entry><entry>VKNQENVVFLFSADWCPDCRVIEPFLPELEQTYDEYQFYYVNRDDFIELCQELDIFGIPS</entry><entry>72</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>FVVVENGQELGRLVNKNRKTKAEITKFLAE</entry><entry>103</entry></row><row><entry /><entry /><entry>F+   NG+E  R V+K+RKTK EI +FL E</entry><entry /></row><row><entry>Sbjct:</entry><entry>73</entry><entry>FLFYSNGEERSRFVSKDRKTKEEIERFLTE</entry><entry>102</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 433&gt; which encodes the amino acid sequence &lt;SEQ ID 434&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00452" num="00452"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1997(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00453" num="00453"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 70/102 (68%), Positives = 81/102 (78%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MILPESYEEIAAYIDSTKKVVFFFTADWCPDCQFIYPVMPSIEKDFSDFVFVRVNRDDYI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MI P SYE +A  I+   K+V FFTADWCPDCQFIYP+MP IE + +D  FV VNRD +I</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MIRPTSYESLATLIEKEDKLVLFFTADWCPDCQFIYPIMPEIEAELTDMTFVCVNRDQFI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>ELAQQWNIFGIPSFVVVENGQELGRLVNKNRKTKAEITKFLA</entry><entry>102</entry></row><row><entry /><entry /><entry>E+AQ+WNIFGIPSFVV+E GQE+GRLVNK RKTK EI  FLA</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>EVAQKWNIFGIPSFVVIEKGQEVGRLVNKMRKTKTEIMHFLA</entry><entry>102</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 128

A DNA sequence (GBSx0133) was identified in <i>S. agalactiae </i>&lt;SEQ ID 435&gt; which encodes the amino acid sequence &lt;SEQ ID 436&gt;. This protein is predicted to be phenylalanyl-tRNA synthetase beta subunit, non-spirochete. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00454" num="00454"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1310(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00455" num="00455"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC00291 GB:AF008220 YtpR [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 78/196 (39%), Positives = 125/196 (62%), Gaps = 1/196 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>YNREHVGDTLMVIVKDSQGAKLDVDRRGQVARVYLQDSKETVAWNIFEVSSLIVIEGAGQ</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>YN+E VGDTL++ ++D    +L  ++ G V +++  ++KET  +NIF  SS + I+  G</entry><entry /></row><row><entry>Sbjct:</entry><entry>5</entry><entry>YNKEGVGDTLLISLQDVTREQLGYEKHGDVVKIFNNETKETTGFNIFNASSYLTIDENGP</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>ITLSDQDIKILNAELLKEGFEDSLVNNIEPTFVVAQIKEIIDHPDSDHLHICQAEINDGK</entry><entry>124</entry></row><row><entry /><entry /><entry>+ LS+  ++ +N  L + G E++LV ++ P FVV  ++    HP++D L +C+  + + +</entry><entry /></row><row><entry>Sbjct:</entry><entry>65</entry><entry>VALSETFVQDVNEILNRNGVEETLVVDLSPKFVVGYVESKEKHPNADKLSVCKVNVGE-E</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>TVQIVCGAPNASVGLKTVAALPGAMMPNGSLIFPGKLRGEDSFGMLCSARELALPNAPQV</entry><entry>184</entry></row><row><entry /><entry /><entry>T+QIVCGAPN   G K V A  GA+MP+G +I   +LRG  S GM+CSA+EL LP+AP</entry><entry /></row><row><entry>Sbjct:</entry><entry>124</entry><entry>TLQIVCGAPNVDQGQKVVVAKVGAVMPSGLVIKDAELRGVPSSGMICSAKELDLPDAPAE</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>RGIIELSDQVIVGESF</entry><entry>200</entry></row><row><entry /><entry /><entry>+GI+ L      G++F</entry><entry /></row><row><entry>Sbjct:</entry><entry>184</entry><entry>KGILVLEGDYEAGDAF</entry><entry>199</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 437&gt; which encodes the amino acid sequence &lt;SEQ ID 438&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00456" num="00456"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="21pt" align="left" /><colspec colname="2" colwidth="49pt" align="left" /><colspec colname="3" colwidth="98pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="91pt" align="left" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.49</entry><entry>Transmembrane</entry><entry>90-106 (90-107)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1595(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00457" num="00457"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB06970 GB: AP001518 phenylalanyl-tRNA synthetase (beta subunit)</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 84/196 (42%), Positives = 124/196 (62%), Gaps = 1/196 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>YNKEQVGDVLMVILQDTKDIKRQVERKGKVARVFAEESGKTLAWNIFEASSLITIEGNGQ</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>YN++ +GD +++++ + +   R  ER+G V R++   +GKT  +N+F AS      G G</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>YNEKGIGDTILIVIDEVEPANRAYERQGDVVRIYHLGTGKTTGYNLFHASKYGEFNGQGL</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>IFLTDENLARLNAELAKEGFSERLEPIVGPVFVVGQIVEMVAHPDSDHLNICQVAIGEDQ</entry><entry>124</entry></row><row><entry /><entry /><entry>+ LTD  +A L     K G +  LE  + P FVVG +     HP++D L+IC+V +G D</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>LELTDSLVATLEQAFQKNGVNWTLEVDLSPKFVVGFVQSKDKHPNADKLSICKVDVGSD-</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>TVQIVAGAPNAALGLKTIVALPGAIMPNGSLIFPGKLRGEESYGMMCSPRELALPNAPQK</entry><entry>184</entry></row><row><entry /><entry /><entry>T+QIV GAPN   G K +VAL GA+MP+G +I P  LRG  S GM+CS +ELALP+AP++</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>TLQIVCGAPNVEAGQKVVVALEGAVMPSGLVIKPTSLRGVSSTGMICSAKELALPDAPEE</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>RGIIEFDESAVVGEAF</entry><entry>200</entry></row><row><entry /><entry /><entry>+GI+  D+S  VG +F</entry></row><row><entry>Sbjct:</entry><entry>184</entry><entry>KGILVLDDSYEVGTSF</entry><entry>199</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00458" num="00458"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 133/207 (64%), Positives = 167/207 (80%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MIFTYNREHVGDTLMVIVKDSQGAKLDVDRRGQVARVYLQDSKETVAWNIFEVSSLIVIE</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MIF YN+E VGD LMVI++D++  K  V+R+G+VARV+ ++S +T+AWNIFE SSLI IE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MIFAYNKEQVGDVLMVILQDTKDIKRQVERKGKVARVFAEESGKTLAWNIFEASSLITIE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GAGQITLSDQDIKILNAELLKEGFEDSLVNNIEPTFVVAQIKEIIDHPDSDHLHICQAEI</entry><entry>120</entry></row><row><entry /><entry /><entry>G GQI L+D+++  LNAEL KEGF + L   + P FVV QI E++ HPDSDHL+ICQ  I</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GNGQIFLTDENLARLNAELAKEGFSERLEPIVGPVFVVGQIVEMVAHPDSDHLNICQVAI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NDGKTVQIVCGAPNASVGLKTVAALPGAMMPNGSLIFPGKLRGEDSFGMLCSARELALPN</entry><entry>180</entry></row><row><entry /><entry /><entry> + +TVQIV GAPNA++GLKT+ ALPGA+MPNGSLIFPGKLRGE+S+GM+CS RELALPN</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GEDQTVQIVAGAPNAALGLKTIVALPGAIMPNGSLIFPGKLRGEESYGMMCSPRELALPN</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>APQVRGIIELSDQVIVGESFDANKHWK</entry><entry>207</entry></row><row><entry /><entry /><entry>APQ RGIIE  +  +VGE+FD  KHWK</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>APQKRGIIEFDESAVVGEAFDPAKHWK</entry><entry>207</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 129

A DNA sequence (GBSx0135) was identified in <i>S. agalactiae </i>&lt;SEQ ID 439&gt; which encodes the amino acid sequence &lt;SEQ ID 440&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00459" num="00459"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3052(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00460" num="00460"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB81904 GB: U92974 unknown [<i>Lactococcus lactis</i>]</entry><entry /></row><row><entry>Identities = 69/241 (28%), Positives = 117/241 (47%), Gaps = 15/241 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>YKEMLAKPWGKIQYEITFAQL--SHIKNQNVLDFGAGFCLTEQHLAKEN-NVTAIEPNPK</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>Y E+  KPWG++ Y++ F QL  +  K+  +L FG+GF  TE  L ++   VT  EP+ +</entry></row><row><entry>Sbjct:</entry><entry>23</entry><entry>YAEVFEKPWGRMFYDLLFPQLLPNLTKDSKILSFGSGFGRTETFLEEQGFEVTGYEPDVE</entry><entry>82</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>LLYDNQSDNIYKILGSYEALRD-LPDQSFDTIICHNVLEYIDKHNHPAYFDEFSRLLKPN</entry><entry>122</entry></row><row><entry /><entry /><entry> L         ++ G+++   + + ++ +D I+ HNVLEY+   +     +    LL</entry></row><row><entry>Sbjct:</entry><entry>83</entry><entry>KLEMMSDQTFRQLTGTFDDFAETVKNERYDVILIHNVLEYV--LDRKVVLELLLSLLTDG</entry><entry>140</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>GELSLIKHNITGKILQSVIFSNDTSTAMELLTGEANFKSASFDQGNIYT-----LEELKQ</entry><entry>177</entry></row><row><entry /><entry /><entry>G LS++KH+  G +++     ++   A+++   EA    AS + G+I       L +</entry></row><row><entry>Sbjct:</entry><entry>141</entry><entry>GTLSIVKHSKYGSMIEMAAGRDNPQAALDVYENEA---VASHNHGDILVYDDDWLTDFVA</entry><entry>197</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>NTNLLVERYQGIRTFYSLQPN-HFKTETGWLNKMLAIELSVADKAPYKDIAFLQHITLKKS</entry><entry>237</entry></row><row><entry /><entry /><entry>N  L ++   GIR FY +  N   K    W   ML +E  VA       +A L H+  KKS</entry></row><row><entry>Sbjct:</entry><entry>198</entry><entry>NYKLKLQEKFGIRHFYGISQNAEIKETENWYQPMLKLEQKVAKDQTLYPVARLHHLIFKKS</entry><entry>258</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 130

A DNA sequence (GBSx0136) was identified in <i>S. agalactiae </i>&lt;SEQ ID 441&gt; which encodes the amino acid sequence &lt;SEQ ID 442&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00461" num="00461"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3479(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00462" num="00462"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF74079 GB: AF212845 putative single stranded binding protein</entry><entry /></row><row><entry>[<i>Lactococcus lactis bacteriophage </i>ul36]</entry></row><row><entry>Identities = 64/141 (45%), Positives = 92/141 (64%), Gaps = 10/141 (7%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYNKVIMIGRLTAKPEMVKTPTDKSVTRATVAVNRRFKGSNGEREADFINVVMWGRLAET</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M N V ++GR+T +PE+  TP +K+V   T+AVNR FK +NGEREADFI+ V+WG+ AE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MINNVTLVGRITKEPELRYTPQNKAVATFTLAVNRAFKNANGEREADFISCVIWGKSAEN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LASYGTKGSLISIDGELRTRKYE-KDGQTHYITEVLASSFQLLESRAQ---------RAM</entry><entry>110</entry></row><row><entry /><entry /><entry>LA++  KG LI + G ++TR YE + GQ  YITEV+AS+FQ+LE   Q          +</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LANWTHKGQLIGVIGNIQTRNYENQQGQRVYITEVVASNFQVLEKSNQANGERISNPASK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>111</entry><entry>RENNVSGDLSDLVLEEEELPF</entry><entry>131</entry></row><row><entry /><entry /><entry> +NN S     + + +++LPF</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PQNNDSFGSDPMEISDDDLPF</entry><entry>141</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 443&gt; which encodes the amino acid sequence &lt;SEQ ID 444&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00463" num="00463"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1817(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00464" num="00464"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 102/131 (77%), Positives = 116/131 (87%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYNKVIMIGRLTAKPEMVKTPTDKSVTRATVAVNRRFKGSNGEREADFINVVMWGRLAET</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MYNKVI IGRL AKPE+VKT TDK V R ++AVNRRFK ++GEREADFI+VV+WG+LAET</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MYNKVIAIGRLVAKPELVKTATDKHVARLSLAVNRRFKNASGEREADFISVVVWGKLAET</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LASYGTKGSLISIDGELRTRKYEKDGQTHYITEVLASSFQLLESRAQRAMRENNVSGDLS</entry><entry>120</entry></row><row><entry /><entry /><entry>L SY +KGSL+SIDGELRTRKY+KDGQ HY+TEVL  SFQLLESRAQRAMRENNV+ DL</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LVSYASKGSLMSIDGELRTRKYDKDGQVHYVTEVLCQSFQLLESRAQRAMRENNVTNDLV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DLVLEEEELPF</entry><entry>131</entry></row><row><entry /><entry /><entry>DLVLEE+ LPF</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>DLVLEEDTLPF</entry><entry>131</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 131

A DNA sequence (GBSx0037) was identified in <i>S. agalactiae </i>&lt;SEQ ID 445&gt; which encodes the amino acid sequence &lt;SEQ ID 446&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00465" num="00465"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2235(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9493&gt; which encodes amino acid sequence &lt;SEQ ID 9494&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00466" num="00466"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAC13072 GB: AL445503 putative hydrolase [<i>Streptomyces</i></entry><entry /></row><row><entry><i>coelicolor</i>]</entry></row><row><entry>Identities = 63/179 (35%), Positives = 91/179 (50%), Gaps = 2/179 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>33</entry><entry>IIFDMDGVIVDSEYTFLDNKTEMLREEGI-DTDVSYQYQYMGTTFEFMWQAMKEEFGLPK</entry><entry>91</entry><entry /></row><row><entry /><entry /><entry>+IFD+DG +VDSE  + +     L E G+ D   +    Y+G + +      K  +GL</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>VIFDLDGTLVDSEPHYYEAGRRTLAEYGVPDFSWADHEAYVGISTQETVADWKRRYGLRA</entry><entry>71</entry></row><row><entry /></row><row><entry>Query:</entry><entry>92</entry><entry>TVKEYIAEMNRRRQAIVARDGVRPIKGAQRLIHWLHQHGYRLAVASSSPMVDIKRNLKEL</entry><entry>151</entry></row><row><entry /><entry /><entry>TV+E +A  NR    + AR   R     ++ +  L   G  +AVAS S    I   L</entry></row><row><entry>Sbjct:</entry><entry>72</entry><entry>TVEELLAVKNRHYLGL-ARTSARAYPEMRKFVELLAGEGVPMAVASGSSPEAIAAILART</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>152</entry><entry>GVTECFEYMVTGEDVSSSKPAPDVFLRAAELLDVDPKVCIVIEDTRNGSLAAKAAGMYC</entry><entry>210</entry></row><row><entry /><entry /><entry>G+      +V+ ++V+  KPAPDVFL AA  L  +P  C+V+ED   G+ AA AAGM C</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>GLDAHLRTVVSADEVARGKPAPDVFLEAARRLGTEPARCVVLEDAAPGAAAAHAAGMRC</entry><entry>189</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 447&gt; which encodes the amino acid sequence &lt;SEQ ID 448&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00467" num="00467"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3706(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00468" num="00468"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 62/202 (30%), Positives = 100/202 (48%), Gaps = 1/202 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>29</entry><entry>MEKVIIFDMDGVIVDSEYTFLDNKTEMLREEGIDTDVSYQYQYMGTTFEFMWQAMKEEFG</entry><entry>88</entry><entry /></row><row><entry /><entry /><entry>M K IIFDMDGV+ D+E  +L  + +  + +GI  D      ++G   + +W+ +  +</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>MIKGIIFDMDGVLFDTEPFYLRRREDFFKTKGIPIDHLNSKDFIGGNLQELWKELLGKNR</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>89</entry><entry>LPKTVKEYIAEMNRRRQAIVARDGVRPIKGAQRLIHWLHQHGYRLAVASSSPMVDIKRNL</entry><entry>148</entry></row><row><entry /><entry /><entry>    VK    + +  +QA         I      +  L + G +LAVAS+S   D+   L</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>DDAIVKAITTDYDAYKQAHKPPYQKLLITEVNSCLEQLEKQGIKLAVASNSKRQDVLLAL</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>149</entry><entry>KELGVTECFEYMVTGEDVSSSKPAPDVFLRAAELLDVDPKVCIVIEDTRNGSLAAKAAGM</entry><entry>208</entry></row><row><entry /><entry /><entry>+   + + FE ++  EDVS  KP PD++ +A + L +  K  +V+ED++ G  AAKAA +</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>ETTQIKDYFEIILAREDVSRGKPYPDIYNKAVQKLGLQKKQLLVVEDSQKGIAAAKAANL</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>209</entry><entry>YCFGFANPDYPPQDLSMADKVI</entry><entry>230</entry></row><row><entry /><entry /><entry>  F   +  Y   D S AD  I</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>TVFAITDYRY-GIDQSQADHKI</entry><entry>203</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 132

A DNA sequence (GBSx0138) was identified in <i>S. agalactiae </i>&lt;SEQ ID 449&gt; which encodes the amino acid sequence &lt;SEQ ID 450&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00469" num="00469"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.22</entry><entry>Transmembrane</entry><entry>16-32 (16-32)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1086(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 133

A DNA sequence (GBSx0139) was identified in <i>S. agalactiae </i>&lt;SEQ ID 451&gt; which encodes the amino acid sequence &lt;SEQ ID 452&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00470" num="00470"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 34</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = 5.04</entry><entry>Transmembrane</entry><entry>28-44 (27-45)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3017(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 134

A DNA sequence (GBSx0140) was identified in <i>S. agalactiae </i>&lt;SEQ ID 453&gt; which encodes the amino acid sequence &lt;SEQ ID 454&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00471" num="00471"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 17</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.72</entry><entry>Transmembrane</entry><entry>  38-54 (34-60)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.70</entry><entry>Transmembrane</entry><entry>   4-20 (1-22)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry>153-169 (150-171)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.55</entry><entry>Transmembrane</entry><entry>179-195 (178-198)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.39</entry><entry>Transmembrane</entry><entry> 93-109 (93-109)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.17</entry><entry>Transmembrane</entry><entry>116-132 (116-133)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.43</entry><entry>Transmembrane</entry><entry>344-360 (344-360)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5288(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00472" num="00472"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14853 GB: Z99118 two-component sensor histidine kinase</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 254/585 (43%), Positives = 371/585 (63%),</entry></row><row><entry>Gaps = 9/585 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>LMVLLFQRLGIIMILAFLLVNNSYFRQLIEERSK-RETVVLVIIFGLFVIISNITGIEIK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>LM+++ +R+GII+IL F+L +   FRQ ++ +   +   +L+ IF LF IISN TGIEI+</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>LMIMMLERVGIIVILGFILAHTKLFRQALQNQDGYKGKAILISIFSLFSIISNYTGIEIQ</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GDRSLVERPFLTTISHSDSLANTRTLVITTASLVGGPLVGSIVGFIGGVHRFFQGSFSGS</entry><entry>120</entry></row><row><entry /><entry /><entry> +  +V   ++ TI  S S+ANTR L +    L+GGP VG+ +G + G+HRF  G  +</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>RNM-IVNNDWVFTIDPSGSIANTRILGVEIGGLLGGPFVGAGIGILAGLHRFSLGGSTAL</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>FYIVSSVLVGIVSGKIGDKLKENHLYPSTSQVILISIIAESIQMLFVGIFT-----GWEL</entry><entry>175</entry></row><row><entry /><entry /><entry>   VSS+L G+++G IG    + +  P+     L+ I  ES+QM+ + +        WEL</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>SCAVSSILAGVLAGLIGRYFTKRYRMPTPRIAALVGIGMESLQMIIILLMAKPFSDAWEL</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>VKMIVIPMMILNSLGSTLFLAILKTYLSNESQLRAVQTRDVLELTRQTLPYLRQGLTPQS</entry><entry>235</entry></row><row><entry /><entry /><entry>V MI IPM+++N  GS +FL+I++  +  E Q RA++T  VL +  QTLP+ RQGL   S</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>VSMIGIPMILINGTGSFIFLSIIQAIIRKEEQARALETHRVLTIADQTLPFFRQGLNENS</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>ARSVCEIIKRHTNFDAVGLTDRSNVLAHIGVGHDHHIAGQPVKTDLSKSVIFDGEPRIAQ</entry><entry>295</entry></row><row><entry /><entry /><entry> +SV  II + T  DAV LTD+  +LAH+G G DHHI, + + T LSK VI  G    A</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>CKSVAAIIHKLTGTDAVSLTDKEKILAHVGAGMDHHIPSKSLITGLSKKVIKTGHIMKAI</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>DKAAISCPDHNCQLNSAIVVPLKINDKTVGALKMYFAGDKTMSEVEENLVLGLAQIFSGQ</entry><entry>355</entry></row><row><entry /><entry /><entry> +  I C    C L++AIV+PL  N  T+G LKMYF     +S+VEE L  GLA +FS Q</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>SQEEIECTHAECPLHAAIVLPLTSNGNTIGTLKMYFKSPAGLSQVEEELAEGLAMLFSTQ</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>LAMGITEEQNKLASMAEIKALQAQINPHFFFNAINTISALIRIDSDKARYALMQLSTFFR</entry><entry>415</entry></row><row><entry /><entry /><entry>L +G  E Q+KL   AEIKALQAQ+NPHF FNAINTISAL R D +K R  L+QLS +FR</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>LELGEAELQSKLLKDAEIKALQAQVNPHFLFNAINTISALCRTDVEKTRKLLLQLSVYFR</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>TSLQGGQDREVTLEQEKSHVDAYMNVEKLRFPDKYQLSYDI-SAPEKMKLPPFGLQVLVE</entry><entry>474</entry></row><row><entry /><entry /><entry>++LQG +   + L +E +H++AY+++E+ RFP KY++  +I S  E++++PPF LQVLVE</entry></row><row><entry>Sbjct:</entry><entry>423</entry><entry>SNLQGARQLLIPLSKELNHLNAYLSLEQARFPGKYKIELNIDSRLEQIEIPPFVLQVLVE</entry><entry>482</entry></row><row><entry /></row><row><entry>Query:</entry><entry>475</entry><entry>NAVRHAFKERKTDNHILVQIKPDGHYYCVSVSDNGQGISDTIIDKLGQETVAESKGTGTA</entry><entry>534</entry></row><row><entry /><entry /><entry>NA+RHAF +++    + V +  D     + V+DNG+GI   ++ +LG++     +GTGTA</entry></row><row><entry>Sbjct:</entry><entry>483</entry><entry>NALRHAFPKKQDICKVTVCVLSDDASVYMKVADNGRGIPPDVLPELGKKPFPSKEGTGTA</entry><entry>542</entry></row><row><entry /></row><row><entry>Query:</entry><entry>535</entry><entry>LVNLNNRLNLLYGSVSCLHFSSD-KNGTKVWYRIPNRIREDEHEN</entry><entry>578</entry></row><row><entry /><entry /><entry>L NLN RL  L+G  + LH SS+   GT+V +++P +  ++  E+</entry></row><row><entry>Sbjct:</entry><entry>543</entry><entry>LYNLNQRLIGLFGQQAALHISSEVHKGTEVSFQVPMQQMKEGEEH</entry><entry>587</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 455&gt; which encodes the amino acid sequence &lt;SEQ ID 456&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00473" num="00473"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1771(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00474" num="00474"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 75/245 (30%), Positives = 117/245 (47%), Gaps = 22/245 (8%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>348</entry><entry>LAQIFSGQL-----AMGITEEQNKLASMAEIKALQAQINPHFFFNAINTISALIRI-DSD</entry><entry>401</entry><entry /></row><row><entry /><entry /><entry>LAQ F+  L      M    ++ K      ++AL +QINPHF +N ++TI  +    DS</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>LAQQFNALLDQIDSLMVAVADKEKAIGQYRLQALASQINPHFLYNTLDTIIWMAEFNDSK</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>402</entry><entry>KARYALMQLSTFFRTSLQGGQDREVTLEQEKSHVDAYMNVEKLRFPDKYQLSYDISAPE-</entry><entry>460</entry></row><row><entry /><entry /><entry>+       L+ +FR +L  G +  + L  E  HV  Y+ ++K R+ DK  LSY++   +</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>RVVEVTKSLAKYFRLALNQGNEY-IRLADELDHVSQYLFIQKQRYGDK--LSYEVQGLDV</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>461</entry><entry>--KMKLPPFGLQVLVENAVRHAFKERKTDNHILVQIKPDGHYYCVSVSDNGQGISDTIID</entry><entry>518</entry></row><row><entry /><entry /><entry>     +P   LQ LVENA+ H  KE      I V +     +  ++V DNG+GI D+ +</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>YADFVIPKLILQPLVENAIYHGIKEVDRKGMIKVTVSDTAQHLMLTVWDNGKGIEDSSLT</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>519</entry><entry>KLGQETVAESKGTGTALVNLNNRLNLLYGS--VSCLHFSSDKNGTKVWYRIPNR---IRE</entry><entry>573</entry></row><row><entry /><entry /><entry>   Q  +A     G  L N++ RL L YG      +H  SD+  T++   +P     + +</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>N-SQSLLARG---GVGLKNVDQRLKLHYGEGYHMTIHSQSDQ-FTEIQLSLPKMHELMAD</entry><entry>235</entry></row><row><entry /></row><row><entry>Query:</entry><entry>574</entry><entry>DEHEN</entry><entry>578</entry></row><row><entry /><entry /><entry>D  EN</entry></row><row><entry>Sbjct:</entry><entry>236</entry><entry>DTQEN</entry><entry>240</entry></row></tbody></tgroup></table></tables>

SEQ ID 454 (GBS248d) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 124</figref> (lane 2-4; MW 71 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 124</figref> (lane 5-7; MW 46 kDa) and in <figref idrefs="DRAWINGS">FIG. 180</figref> (lane 2; MW 46 kDa).

GBS248d-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 234</figref>, lane 3-4.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 135

A DNA sequence (GBSx0141) was identified in <i>S. agalactiae </i>&lt;SEQ ID 457&gt; which encodes the amino acid sequence &lt;SEQ ID 458&gt;. This protein is predicted to be two-component response regulator (lytT). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00475" num="00475"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3230(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9495&gt; which encodes amino acid sequence &lt;SEQ ID 9496&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00476" num="00476"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14852 GB: Z99118 two-component response</entry><entry /></row><row><entry>regulator [<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 105/244 (43%), Positives = 157/244 (64%),</entry></row><row><entry>Gaps = 6/244 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MKILILDDEMFARQELSFLVEHSQEVDNPEIFQAEDISEAEKILFRQQIDLIFLDISLSE</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>+++LI+DDEM AR EL++L++ +   D  EI +AE+I  A   +  Q+ DL+FLD+ LS</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>LRVLIVDDEMLARDELAYLLKRTN--DEMEINEAENIESAFDQMMDQKPDLLFLDVDLSG</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>ENGFTLANQLSQLAHPPLVVFATAYDNYAVKAFESNAVDYIMKPFEQQRVDMALSKVKKL</entry><entry>122</entry></row><row><entry /><entry /><entry>ENGF +A +L ++ HPP +VFATAYD YA+KAFE +A+DY+ KPF+++R+   L K KK+</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>ENGFDIAKRLKKMKHPPAIVFATAYDQYALKAFEVDALDYLTKPFDEERIQQTLKKYKKV</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>SQLTTASDVEQAIPKKASVELLTLTLSDRSVVVKMQDIVAASVEDGELTVSTVQKTYTIR</entry><entry>182</entry></row><row><entry /><entry /><entry>++      VE      A    L L++ +  V+V  +DI+ A  EDG + V T   +YT+</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>NR----DIVETEQNSHAGQHKLALSVGESIVIVDTKDIIYAGTEDGHVNVKTFDHSYTVS</entry><entry>175</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>KTLNWFKSRAVAPYFLQIHRNTVINLEMIEEIQPWFNHTLLLIMSNGEKFPVGRSYLKDL</entry><entry>242</entry></row><row><entry /><entry /><entry> TL   + +     F+++HR+ V+N E I+EIQPWFN T  LIM +G K PV R+Y K+L</entry></row><row><entry>Sbjct:</entry><entry>176</entry><entry>DTLVVIEKKLPDSDFIRVHRSFVVNTEYIKEIQPWFNSTYNLIMKDGSKIPVSRTYAKEL</entry><entry>235</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>NEHL</entry><entry>246</entry></row><row><entry /><entry /><entry> + L</entry></row><row><entry>Sbjct:</entry><entry>236</entry><entry>KKLL</entry><entry>239</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 459&gt; which encodes the amino acid sequence &lt;SEQ ID 460&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00477" num="00477"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3818(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00478" num="00478"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 44/148 (29%), Positives = 84/148 (56%), Gaps = 5/148 (3%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>ILILDDEMFARQELSFLVEHSQ-EVDNPEIFQAEDISEAEKILFRQQIDLIFLDISLSEE</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>+LI++DE   RQ +  LV+ SQ ++D   + +AE+   A  +  ++  D++  DI++ +</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>LLIVEDEYLVRQGIRSLVDFSQFKIDR--VNEAENGQLAWDLFQKEPYDIVLTDINMPKL</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>NGFTLANQLSQLAHPPLVVFATAYD--NYAVKAFESNAVDYIMKPFEQQRVDMALSKVKK</entry><entry>121</entry></row><row><entry /><entry /><entry>NG  LA  + Q +    +VF T YD  NYA+ A +  A DY++KPF +  V+  L K++K</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>NGIQLAELIKQESPQTHLVFLTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRK</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>LSQLTTASDVEQAIPKKASVELLTLTLS</entry><entry>149</entry></row><row><entry /><entry /><entry>  +L+  ++  Q + ++   E+  + ++</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>KLELSKKTETIQELVEQPQKEVSAIAMA</entry><entry>149</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 136

A DNA sequence (GBSx0142) was identified in <i>S. agalactiae </i>&lt;SEQ ID 461&gt; which encodes the amino acid sequence &lt;SEQ ID 462&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00479" num="00479"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0266(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 137

A DNA sequence (GBSx0143) was identified in <i>S. agalactiae </i>&lt;SEQ ID 463&gt; which encodes the amino acid sequence &lt;SEQ ID 464&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00480" num="00480"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.89</entry><entry>Transmembrane</entry><entry>104-120 (99-134)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.89</entry><entry>Transmembrane</entry><entry>  47-63 (46-65)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.29</entry><entry>Transmembrane</entry><entry>  22-38 (21-39)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.81</entry><entry>Transmembrane</entry><entry>  74-90 (70-92)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5755(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8499&gt; which encodes amino acid sequence &lt;SEQ ID 8500&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00481" num="00481"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14851 GB: Z99118 similar to hypothetical proteins from</entry><entry /></row><row><entry><i>B. subtilis </i>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 50/110 (45%), Positives = 82/110 (74%),</entry></row><row><entry>Gaps = 2/110 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>20</entry><entry>QMSIYAAILLVSQMISMLLPKSLPIPTTVIGLVLMYVLLTAKIIKVEWVDSFGALMISMI</entry><entry>79</entry><entry /></row><row><entry /><entry /><entry>Q  I+A I+LVS MI+ ++P  +PIP +V+GLVL+++LL  K+IK+E V++ G  + S+I</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>QAFIFAVIMLVSNMIAAIVP--IPIPASVVGLVLLFLLLCLKVIKLEQVETLGTSLTSLI</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>80</entry><entry>GFMFVPSGISVAANLDILKAEGLQLVAVITISTVVMLVVVAYVARLILAI</entry><entry>129</entry></row><row><entry /><entry /><entry>GF+FVPSGISV  +L +++  GLQ+V VI ++T+++L      ++LIL++</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>GFLFVPSGISVMNSLGVMQQYGLQIVLVILLATIILLGATGLFSQLILSL</entry><entry>119</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 138

A DNA sequence (GBSx0144) was identified in <i>S. agalactiae </i>&lt;SEQ ID 465&gt; which encodes the amino acid sequence &lt;SEQ ID 466&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00482" num="00482"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="21pt" align="left" /><colspec colname="6" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −12.21</entry><entry>Transmembrane</entry><entry>219-235 (208-241)</entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −11.94</entry><entry>Transmembrane</entry><entry>103-119 (99-133) </entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.57</entry><entry>Transmembrane</entry><entry>157-173 (154-175)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.70</entry><entry>Transmembrane</entry><entry>73-89 (73-89)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.5883 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00483" num="00483"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB14850 GB: Z99118 similar to hypothetical proteins [<i>Bacillus</i></entry><entry /></row><row><entry><i>subtilis</i>]</entry></row><row><entry>Identities = 120/240 (50%), Positives = 159/240 (66%), Gaps = 10/240 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MELLKTPIFGICFSLILYTIGEHLFKKSKGFFLLQPLFFAMVSGIVILWLMSKGLGTDVK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>ME   +P FGI  SL  + IG  LFKK+KGFFL  PLF AMV GI  L          +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MESTMSPYFGIVVSLAAFGIGTFLFKKTKGFFLFTPLFVAMVLGIAFL---------KIG</entry><entry>51</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TFYTQAYKPGGDLIFWFLNPATIAFAVPLYKKNDVVKKYWVEILSSLVIGMIVSLILIVA</entry><entry>120</entry></row><row><entry /><entry /><entry> F    Y  GG++I +FL PATIAFA+PLYK+ D +KKYW +I++S++ G I S+ ++</entry></row><row><entry>Sbjct:</entry><entry>52</entry><entry>GFSYADYNNGGEIIKFFLEPATIAFAIPLYKQRDKLKKYWWQIMASIIAGSICSVTIVYL</entry><entry>111</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>ISKMVGLSQVGIASMLPQAATTAIALPITAAIGGNTAVTAMACILNAVIIYALGKKLVSF</entry><entry>180</entry></row><row><entry /><entry /><entry>++K + L    + SMLPQAATTAIALP++  IGG + +TA A I NAVI+YALG   +</entry></row><row><entry>Sbjct:</entry><entry>112</entry><entry>LAKGIHLDSAVMKSMLPQAATTAIALPLSKGIGGISDITAFAVIFNAVIVYALGALFLKV</entry><entry>171</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>FHLNDSKIGAGLGLGTSGHTVGAAFALELGELQGAMAAIAVVVIGLVVDLVIPIFSHLIG</entry><entry>240</entry></row><row><entry /><entry /><entry>F +  + I  GL LGTSGH +G A  +E+GE++ AMA+IAVVV+G+V  LVIP+F  LIG</entry></row><row><entry>Sbjct:</entry><entry>172</entry><entry>FKVK-NPISKGLALGTSGHALGVAVGIEMGEVEAAMASIAVVVVGVVTVLVIPVFVQLIG</entry><entry>230</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 139

A DNA sequence (GBSx0145) was identified in <i>S. agalactiae </i>&lt;SEQ ID 467&gt; which encodes the amino acid sequence &lt;SEQ ID 468&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00484" num="00484"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="266pt" align="left" /><colspec colname="2" colwidth="175pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00485" num="00485"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 508/542 (93%), Positives = 523/542 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTKYLKYISFVALFLASIFLVACQNQNSQTKERTRKQRPKDELVVSMGAKLPHEFDPKDR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>++KYLKY S + LFL  + LVACQ Q  QTKER RKQRPKDELVVSMGAKLPHEFDPKDR</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>VSKYLKYFSIITLFLTGLILVACQQQKPQTKERQRKQRPKDELVVSMGAKLPHEFDPKDR</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YGIHNEGNITHSTLLKRSPELDIKGELAKKYKISKDGLTWSFDLNDDFKFSNGEPVTADD</entry><entry>120</entry></row><row><entry /><entry /><entry>YG+HNEGNITHSTLLKRSPELDIKGELAK Y +S+DGLTWSFDL+DDFKFSNGEPVTADD</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>YGVHNEGNITHSTLLKRSPELDIKGELAKTYHLSEDGLTWSFDLHDDFKFSNGEPVTADD</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK</entry><entry>180</entry></row><row><entry /><entry /><entry>VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD</entry><entry>240</entry></row><row><entry /><entry /><entry>YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>MIYATPELASKKVKGTRLLDIASNDVRGLSLPYVKKGVVKNSPDGYPVGNDVTSDPAIRK</entry><entry>300</entry></row><row><entry /><entry /><entry>MIYATPELA KKVKGTRLLDI SNDVRGLSLPYVKKGV+ +SPDGYPVGNDVTSDPAIRK</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>MIYATPELADKKVKGTRLLDIPSNDVRGLSLPYVKKGVITDSPDGYPVGNDVTSDPAIRK</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>ALTIGLNRQKVLDTVLNGYGKPAYSIIDRTPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA</entry><entry>360</entry></row><row><entry /><entry /><entry>ALTIGLNRQKVLDTVLNGYGKPAYSIID+TPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>ALTIGLNRQKVLDTVLNGYGKPAYSIIDKTPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>DGSRKKGNLKSEFDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA</entry><entry>420</entry></row><row><entry /><entry /><entry>DGSRKKG+L + FDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>DGSRKKGDLDAAFDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>LLYAGGRHHAQQFYESHYPSLAGKGWTNITFYNNPTVTKYLDKAMTSPDLDKANKYWKLA</entry><entry>480</entry></row><row><entry /><entry /><entry>LLYAGGRHHAQQFYESH+PSLAGKGWTNITFYNNPTVTKYLDKAMTS DLDKAN+YWKLA</entry></row><row><entry>Sbjct:</entry><entry>423</entry><entry>LLYAGGRHHAQQFYESHHPSLAGKGWTNITFYNNPTVTKYLDKAMTSSDLDKANEYWKLA</entry><entry>482</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES</entry><entry>540</entry></row><row><entry /><entry /><entry>QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES</entry></row><row><entry>Sbjct:</entry><entry>483</entry><entry>QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES</entry><entry>542</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>AK</entry><entry>542</entry></row><row><entry /><entry /><entry> K</entry></row><row><entry>Sbjct:</entry><entry>543</entry><entry>TK</entry><entry>544</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 60.

A related GBS gene &lt;SEQ ID 8501&gt; and protein &lt;SEQ ID 8502&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00486" num="00486"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: 22 Crend: 5</entry><entry /></row><row><entry>McG: Discrim Score: 10.46</entry></row><row><entry>GvH: Signal Score (−7.5): −1.29</entry></row><row><entry>Possible site: 22</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="49pt" align="left" /><colspec colname="4" colwidth="133pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 0</entry><entry>value: 7.27</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 7.27</entry><entry>386</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: −1.95</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside -- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 8502 (GBS106) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 18</figref> (lane 3; MW 61 kDa).

The GBS106-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 194</figref>, lane 2) and used to immunise mice. The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 255A</figref>), FACS (<figref idrefs="DRAWINGS">FIG. 255B</figref>), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 140

A DNA sequence (GBSx0146) was identified in <i>S. agalactiae </i>&lt;SEQ ID 469&gt; which encodes the amino acid sequence &lt;SEQ ID 470&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00487" num="00487"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.4862 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 141

A DNA sequence (GBSx0147) was identified in <i>S. agalactiae </i>&lt;SEQ ID 471&gt; which encodes the amino acid sequence &lt;SEQ ID 472&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00488" num="00488"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="center" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −7.27</entry><entry>Transmembrane</entry><entry>252-268 (249-275)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.73</entry><entry>Transmembrane</entry><entry>67-83 (62-90)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.26</entry><entry>Transmembrane</entry><entry>107-123 (104-134)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry>153-169 (152-170)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.3909 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9295&gt; which encodes amino acid sequence &lt;SEQ ID 9296&gt; was also identified.

The protein differs from U78968 at the N-terminus:

<tables id="TABLE-US-00489" num="00489"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MASVNYDTSLTPVQYKAIAHHYGLDKPAPVQYFIWLKNFIQGHLGTSLVYRQPVIDIIRS</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MASVNYDTSLTP QYKAIAHHYGLDKPA VQYFIWLKN IQG LGTSLVYRQPV DIIRS</entry></row><row><entry>Sbjct:</entry><entry>39</entry><entry>MASVNYDTSLTPAQYKAIAHHYGLDKPALVQYFIWLKNVIQGDLGTSLVYRQPVSDIIRS</entry><entry>98</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 64.

A related GBS gene &lt;SEQ ID 8471&gt; and protein &lt;SEQ ID 8472&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00490" num="00490"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: 3.72</entry></row><row><entry>GvH: Signal Score (−7.5): −5.37</entry></row><row><entry>Possible site: 40</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 5</entry><entry>value: −7.27</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="center" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −7.27</entry><entry>Transmembrane</entry><entry>290-306 (287-313)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.89</entry><entry>Transmembrane</entry><entry>12-28 (11-33)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.73</entry><entry>Transmembrane</entry><entry>105-121 (100-128)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.26</entry><entry>Transmembrane</entry><entry>145-161 (142-172)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry>191-207 (190-208)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 2.97</entry><entry>245</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 1.95</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial membrane --- Certainty = 0.3909 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 8472 (GBS436) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 173</figref> (lane 9; MW 54 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 142

A DNA sequence (GBSx0148) was identified in <i>S. agalactiae </i>&lt;SEQ ID 473&gt; which encodes the amino acid sequence &lt;SEQ ID 474&gt;. This protein is predicted to be transmembrane transport protein DppC (oppC). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00491" num="00491"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.28</entry><entry>Transmembrane</entry><entry>  77-93 (68-101)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.80</entry><entry>Transmembrane</entry><entry>182-198 (180-204)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.06</entry><entry>Transmembrane</entry><entry>112-128 (104-132)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.10</entry><entry>Transmembrane</entry><entry>239-255 (235-258)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4312(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

There is homology to SEQ ID 68.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 143

A DNA sequence (GBSx0149) was identified in <i>S. agalactiae </i>&lt;SEQ ID 475&gt; which encodes the amino acid sequence &lt;SEQ ID 476&gt;. This protein is predicted to be ATPase protein DppD. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00492" num="00492"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1957(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein differs from U78968 at the C-terminus:

<tables id="TABLE-US-00493" num="00493"><table frame="none" colsep="0" rowsep="0" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="28pt" align="center" /><colspec colname="3" colwidth="119pt" align="left" /><colspec colname="4" colwidth="28pt" align="center" /><colspec colname="5" colwidth="0pt" align="left" /><tbody valign="top"><row><entry /><entry>Query:</entry><entry>241</entry><entry>QTEFARSLWRSLPQQEFLKGVTHDLRG</entry><entry>267</entry><entry /></row><row><entry /><entry /><entry /><entry>QTEFAR LWR+LPQQ+FLKGVTHDLRG</entry></row><row><entry /><entry>Sbjct:</entry><entry>241</entry><entry>QTEFARRLWRTLPQQDFLKGVTHDLRG</entry><entry>267</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 477&gt; which encodes the amino acid sequence &lt;SEQ ID 478&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00494" num="00494"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1957(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00495" num="00495"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 255/267 (95%), Positives = 262/267 (97%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLEIKKGELLAIIGASGSGKSLLAHAI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLE+KKGELLAIIGASGSGKSLLAHAI</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLEVKKGELLAIIGASGSGKSLLAHAI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>MDILPKNASVTGDMIYRGQSLNSKRIKQLRGKDITLIPQSVNYLDPSTKVKHQVRLGISE</entry><entry>120</entry></row><row><entry /><entry /><entry>MDILPKNA+VTGDMIYRGQSL SKRIKQLRGK++TLIPQSVNYLDPS KVKHQVRLGISE</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>MDILPKNAAVTGDMIYRGQSLTSKRIKQLRGKEMTLIPQSVNYLDPSMKVKHQVRLGISE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NSKATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISDKVSLIIADEPTPGLHPD</entry><entry>180</entry></row><row><entry /><entry /><entry>N+KATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISD VSLIIADEPTPGLHPD</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NAKATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISDTVSLIIADEPTPGLHPD</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSGNGEQL</entry><entry>240</entry></row><row><entry /><entry /><entry>ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSG GEQL</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSGGGEQL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>QTEFARSLWRSLPQQEFLKGVTHDLRG</entry><entry>267</entry></row><row><entry /><entry /><entry>QTEFAR LWR+LPQQ+FLKGVTHDLRG</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>QTEFARRLWRTLPQQDFLKGVTHDLRG</entry><entry>267</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 144

A DNA sequence (GBSx0150) was identified in <i>S. agalactiae </i>&lt;SEQ ID 479&gt; which encodes the amino acid sequence &lt;SEQ ID 480&gt;. This protein is predicted to be ATPase protein DppE. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00496" num="00496"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3783(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 481&gt; which encodes the amino acid sequence &lt;SEQ ID 482&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00497" num="00497"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3383(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00498" num="00498"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 188/205 (91%), Positives = 197/205 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTLEAKKLGFYHKKDQWLFKEINLEVAPGQVLGIFGQSGCGKTSLSRVLAGFLHPKSGEV</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTLEAKKLGFYHKKDQWLFKEI+LEVAPGQ+LGIFGQSGCGKTSLSRVLAGFL PKSGEV</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTLEAKKLGFYHKKDQWLFKEIDLEVAPGQILGIFGQSGCGKTSLSRVLAGFLQPKSGEV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>LVDGSNLPSKAFRPVQLIQQHPEKTMNPLWPMKKSLEEAYYPSRDLLDAFGIQEKWLNRR</entry><entry>120</entry></row><row><entry /><entry /><entry>LVDGS+LP+KAFRPVQLIQQHPE+TMNPLWPMKKSLEEAYYPS+DL DAFGIQEKWL RR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LVDGSHLPNKAFRPVQLIQQHPEQTMNPLWPMKKSLEEAYYPSQDLRDAFGIQEKWLKRR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLIVI</entry><entry>180</entry></row><row><entry /><entry /><entry>PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLI+I</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLIII</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SHDFAMLEKLCNQCYMIEENRIVSF</entry><entry>205</entry></row><row><entry /><entry /><entry>SH+F MLEKLC+ CYMIEENR   F</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SHEFDMLEKLCDACYMIEENRTQLF</entry><entry>205</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 145

A DNA sequence (GBSx0151) was identified in <i>S. agalactiae </i>&lt;SEQ ID 483&gt; which encodes the amino acid sequence &lt;SEQ ID 484&gt;. This protein is predicted to be PTS system, trehalose-specific IIBC component (treB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00499" num="00499"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.14</entry><entry>Transmembrane</entry><entry>468-484 (462-489)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.23</entry><entry>Transmembrane</entry><entry>279-295 (275-306)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.05</entry><entry>Transmembrane</entry><entry>112-128 (105-130)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.35</entry><entry>Transmembrane</entry><entry>204-220 (203-222)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.75</entry><entry>Transmembrane</entry><entry>255-271 (255-271)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.54</entry><entry>Transmembrane</entry><entry>327-343 (326-344)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.37</entry><entry>Transmembrane</entry><entry>422-438 (422-438)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.06</entry><entry>Transmembrane</entry><entry>304-320 (304-320)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5055(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00500" num="00500"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF94072 GB: AE004175 PTS system, trehalose-specific IIBC</entry><entry /></row><row><entry>component [<i>Vibrio cholerae</i>]</entry></row><row><entry>Identities = 225/484 (46%), Positives = 318/484 (65%), Gaps = 28/484 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>KHDAKALLEAIGGKENISAVTHCATRMRFVLNDSSKAKVKVIEELPSVKGTFTNAGQFQV</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>K D   L+E +GG+ NI++VTHC TR+RFVLN   +A    +E L  VKG FTNAGQFQV</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>KQDVTRLIELVGGESNIASVTHCLTRLRFVLNQPEQADKAGLEALSMVKGCFTNAGQFQV</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>IIGNDVPIFYNAFVAVSGIEGVSKEAAKSAAQKNQNPLQRVLTMLAEIFTPIIPAIIVGG</entry><entry>124</entry></row><row><entry /><entry /><entry>+IG +V   Y   +  +G + VSK+ AK AA++N N L+R ++ LAEIF P++PAII GG</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>VIGTEVDQVYKMLLEQTGKQAVSKDDAKVAARQNMNVLERGISHLAEIFVPLLPAIITGG</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LILGFRNILDAVPFEFLGQKVVDGVRQVDSSGHPIWNTLVDVSTFWSGVDSFLWLPGEAI</entry><entry>184</entry></row><row><entry /><entry /><entry>LILGFRN++  +       ++ DG             TL ++S FW+ V +FLWL GEAI</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>LILGFRNVIGDI-------RMFDG------------KTLTEISQFWASVHAFLWLIGEAI</entry><entry>170</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>FHFLPVGIVWSVTRKMGTTQILGIVLGICLVSPQLLNAYSVASTSAADIAKNWSWNFGYF</entry><entry>244</entry></row><row><entry /><entry /><entry>F FLPVG+ WS  +K+G T ILGI LG+ LVSPQL+NAY +             W+FG F</entry></row><row><entry>Sbjct:</entry><entry>171</entry><entry>FFFLPVGVCWSTVKKLGGTPILGITLGVTLVSPQLMNAYLIGKEVPE------VWDFGLF</entry><entry>224</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>TVQKIGYQAQVIPALLAGLSLSYLEIFWRKHIPEVVSMIFVPFLSLVPAIILAHTVLGPI</entry><entry>304</entry></row><row><entry /><entry /><entry> ++K+GYQAQVIPA+LAG++L+++E   R+ +P  + ++ VPF+S++ +++LAH  +GP</entry></row><row><entry>Sbjct:</entry><entry>225</entry><entry>AIEKVGYQAQVIPAILAGVALAFIENNLRRVVPSYLYLVVVPFVSIIVSVVLAHAFIGPF</entry><entry>284</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>GWTLGKWISAIVLIGLTGPVKWLFGAIFGALYAPFVITGLHHMTNAIDTQLIADTKTHTT</entry><entry>364</entry></row><row><entry /><entry /><entry>G  +G  ++      +TG    +   +FG +YAP VITG+HH TNA+D QL+ +     T</entry></row><row><entry>Sbjct:</entry><entry>285</entry><entry>GRVIGDGVAFAAKAAMTGDFAVIGSTLFGFMYAPLVITGIHHTTNAVDLQLMQE--LGGT</entry><entry>342</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>GLWPMIALSNIAQGSAVLAYYFMHRHDEKEAQISLPAAISAYLGVTEPALFGVNVKYIYP</entry><entry>424</entry></row><row><entry /><entry /><entry> +WP+IALSNIAQ SAV+    + +  + E  IS+PAAISAYLGVTEPA++G+N+KY +P</entry></row><row><entry>Sbjct:</entry><entry>343</entry><entry>PIWPLIALSNIAQASAVVGIIIISK-KQGERDISVPAAISAYLGVTEPAMYGINLKYKFP</entry><entry>401</entry></row><row><entry /></row><row><entry>Query:</entry><entry>425</entry><entry>FVAGMIGSSVAGLLATTFNVQANSIGVGGLPGFLSINVKYMGYFFICMAVAIFIPLFLTL</entry><entry>484</entry></row><row><entry /><entry /><entry> ++ MIGS++A  +  +  V AN IGVGGLPG LSI  ++   + + M +AI +P  LTL</entry></row><row><entry>Sbjct:</entry><entry>402</entry><entry>MLSAMIGSALAAAVCGSAGVMANGIGVGGLPGILSIQPQFWSIYLVAMLIAILVPAALTL</entry><entry>461</entry></row><row><entry /></row><row><entry>Query:</entry><entry>485</entry><entry>FFKK</entry><entry>488</entry></row><row><entry /><entry /><entry>   K</entry></row><row><entry>Sbjct:</entry><entry>462</entry><entry>LMYK</entry><entry>465</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 485&gt; which encodes the amino acid sequence &lt;SEQ ID 486&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00501" num="00501"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.61</entry><entry>Transmembrane</entry><entry>466-482 (457-488)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.01</entry><entry>Transmembrane</entry><entry>279-295 (275-306)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.05</entry><entry>Transmembrane</entry><entry>112-128 (105-130)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.35</entry><entry>Transmembrane</entry><entry>204-220 (203-222)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.13</entry><entry>Transmembrane</entry><entry>255-271 (255-272)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.07</entry><entry>Transmembrane</entry><entry>327-343 (325-344)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.59</entry><entry>Transmembrane</entry><entry>422-438 (422-438)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4843(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00502" num="00502"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF94072 GB: AE004175 PTS system, trehalose-specific IIBC</entry><entry /></row><row><entry>component [<i>Vibrio cholerae</i>]</entry></row><row><entry>Identities = 231/484 (47%), Positives = 322/484 (65%), Gaps = 28/484 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>EQDAKSLLTAIGGKENIKVVTHCATRMRFVLNDNNKANVKEIEKISVVKGTFTNAGQFQV</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>+QD   L+  +GG+ NI  VTHC TR+RFVLN   +A+   +E +S+VKG FTNAGQFQV</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>KQDVTRLIELVGGESNIASVTHCLTRLRFVLNQPEQADKAGLEALSMVKGCFTNAGQFQV</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>IIGNDVPVFYNDFTAVSSIEGVSKEAAKSAAKSNQNALQRVMTMLAEIFTPIIPAIIVGG</entry><entry>124</entry></row><row><entry /><entry /><entry>+IG +V   Y      +  + VSK+ AK AA+ N N L+R ++ LAEIF P++PAII GG</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>VIGTEVDQVYKMLLEQTGKQAVSKDDAKVAARQNMNVLERGISHLAEIFVPLLPAIITGG</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LILGFRNILESVPFEFLGQQVEKGKLVFDAAGDPVWNTIVRVSPFWSGVNHFLWLPGEAI</entry><entry>184</entry></row><row><entry /><entry /><entry>LILGFRN++  +              +FD        T+  +S FW+ V+ FLWL GEAI</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>LILGFRNVIGDI-------------RMFDG------KTLTEISQFWASVHAFLWLIGEAI</entry><entry>170</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>FHFLPVGITWSVTRKMGTTQILGIVLGICLVSPQLLNAYAVAGTPAAEIAKNWVWDFGFF</entry><entry>244</entry></row><row><entry /><entry /><entry>F FLPVG+ WS  +K+G T ILGI LG+ LVSPQL+NAY + G    E     VWDFG F</entry></row><row><entry>Sbjct:</entry><entry>171</entry><entry>FFFLPVGVCWSTVKKLGGTPILGITLGVTLVSPQLMNAYLI-GKEVPE-----VWDFGLF</entry><entry>224</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>TINRIGYQAQVIPALLAGLSLAYLEIFWRKRIPEVVSMIFVPFLSLIPALILAHTVLGPI</entry><entry>304</entry></row><row><entry /><entry /><entry> I ++GYQAQVIPA+LAG++LA++E   R+ +P  + ++ VPF+S+I +++LAH  +GP</entry></row><row><entry>Sbjct:</entry><entry>225</entry><entry>AIEKVGYQAQVIPAILAGVALAFIENNLRRVVPSYLYLVVVPFVSIIVSVVLAHAFIGPF</entry><entry>284</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>GWTIGKGISFVVLAGLTGPVKWLFGAIFGALYAPLVITGLHHMTNAIDTQLIADTATRTT</entry><entry>364</entry></row><row><entry /><entry /><entry>G  IG G++F   A +TG    +   +FG +YAPLVITG+HH TNA+D QL+ +     T</entry></row><row><entry>Sbjct:</entry><entry>285</entry><entry>GRVIGDGVAFAAKAAMTGDFAVIGSTLFGFMYAPLVITGIHHTTNAVDLQLMQELG--GT</entry><entry>342</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>GLWPMIALSNIAQGSAVFAYYLMNRHEEREAEISLPAAISAYLGVTEPALFGVNVKYVYP</entry><entry>424</entry></row><row><entry /><entry /><entry> +WP+IALSNIAQ SAV    ++++ ++ E +IS+PAAISAYLGVTEPA++G+N+KY +P</entry></row><row><entry>Sbjct:</entry><entry>343</entry><entry>PIWPLIALSNIAQASAVVGIIIISK-KQGERDISVPAAISAYLGVTEPAMYGINLKYKFP</entry><entry>401</entry></row><row><entry /></row><row><entry>Query:</entry><entry>425</entry><entry>FVAGMIGSGIAGLLSTTFNVQANSIGVGGLPGFMAINVKYMIPFFICMAVAIVVPMFLTF</entry><entry>484</entry></row><row><entry /><entry /><entry> ++ MIGS +A  +  +  V AN IGVGGLPG ++I  ++   + + M +AI+VP  LT</entry></row><row><entry>Sbjct:</entry><entry>402</entry><entry>MLSAMIGSALAAAVCGSAGVMANGIGVGGLPGILSIQPQFWSIYLVAMLIAILVPAALTL</entry><entry>461</entry></row><row><entry /></row><row><entry>Query:</entry><entry>485</entry><entry>FFRK</entry><entry>488</entry></row><row><entry /><entry /><entry>   K</entry></row><row><entry>Sbjct:</entry><entry>462</entry><entry>LMYK</entry><entry>465</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00503" num="00503"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 501/675 (74%), Positives = 573/675 (84%), Gaps = 2/675 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEQFKHDAKALLEAIGGKENISAVTHCATRMRFVLNDSSKAKVKVIEELPSVKGTFTNAG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M +F+ DAK+LL AIGGKENI  VTHCATRMRFVLND++KA VK IE++  VKGTFTNAG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MGKFEQDAKSLLTAIGGKENIKVVTHCATRMRFVLNDNNKANVKEIEKISVVKGTFTNAG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>QFQVIIGNDVPIFYNAFVAVSGIEGVSKEAAKSAAQKNQNPLQRVLTMLAEIFTPIIPAI</entry><entry>120</entry></row><row><entry /><entry /><entry>QFQVIIGNDVP+FYN F AVS IEGVSKEAAKSAA+ NQN LQRV+TMLAEIFTPIIPAI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QFQVIIGNDVPVFYNDFTAVSSIEGVSKEAAKSAAKSNQNALQRVMTMLAEIFTPIIPAI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IVGGLILGFRNILDAVPFEFLGQRVVDGVRQVDSSGHPIWNTLVDVSTFWSGVDSFLWLP</entry><entry>180</entry></row><row><entry /><entry /><entry>IVGGLILGFRNIL++VPFEFLGQ+V  G    D++G P+WNT+V VS FWSGV+ FLWLP</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IVGGLILGFRNILESVPFEFLGQQVEKGKLVFDAAGDPVWNTIVRVSPFWSGVNHFLWLP</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>GEAIFHFLPVGIVWSVTRKMGTTQILGIVLGICLVSPQLLNAYSVASTSAADIAKNWSWN</entry><entry>240</entry></row><row><entry /><entry /><entry>GEAIFHFLPVGI WSVTRKNGTTQILGIVLGICLVSPQLLNAY+VA T AA+IAKNW W+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>GEAIFHFLPVGITWSVTRKMGTTQILGIVLGICLVSPQLLNAYAVAGTPAAEIAKNWVWD</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>FGYFTVQKIGYQAQVIPALLAGLSLSYLEIFWRKHIPEVVSMIFVPFLSLVPAIILAHTV</entry><entry>300</entry></row><row><entry /><entry /><entry>FG+FT+ +IGYQAQVIPALLAGLSL+YLEIFWRK IPEVVSMIFVPFLSL+PA+ILAHTV</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>FGFFTINRIGYQAQVIPALLAGLSLAYLEIFWRKRIPEVVSMIFVPFLSLIPALILAHTV</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>LGPIGWTLGKWISAIVLIGLTGPVKWLFGAIFGALYAPFVITGLHHMTNAIDTQLIADTK</entry><entry>360</entry></row><row><entry /><entry /><entry>LGPIGWT+GK IS +VL GLTGPVKWLFGAIFGALYAP VITGLHHMTNAIDTQLIADT</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LGPIGWTIGKGISFVVLAGLTGPVKWLFGAIFGALYAPLVITGLHHMTNAIDTQLIADTA</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>THTTGLWPMIALSNIAQGSAVLAYYFMHRHDEKEAQISLPAAISAYLGVTEPALFGVNVK</entry><entry>420</entry></row><row><entry /><entry /><entry>T TTGLWPMIALSNIAQGSAV AYY M+RH+E+EA+ISLPAAISAYLGVTEPALFGVNVK</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>TRTTGLWPMIALSNIAQGSAVFAYYLMNRHEEREAEISLPAAISAYLGVTEPALFGVNVK</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>YIYPFVAGMIGSSVAGLLATTFNVQANSIGVGGLPGFLSINVKYMGYFFICMAVAIFIPL</entry><entry>480</entry></row><row><entry /><entry /><entry>Y+YPFVAGMIGS +AGLL+TTFNVQANSIGVGGLPGF++INVKYM  FFICMAVAI +P+</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>YVYPFVAGMIGSGIAGLLSTTFNVQANSIGVGGLPGFMAINVKYMIPFFICMAVAIVVPM</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>FLTLFFKKSGILTKTEEEKLVPDAVIASTTETKSAKEKAVVSGTKLSVVSPLSGLAKPLD</entry><entry>540</entry></row><row><entry /><entry /><entry>FLT FF+KS I+TKTE+E  +P+  + S     +A  K  + GT +++ SPL+G  K L</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>FLTFFFRKSHIMTKTEDEAKLPETPV-SDAPVATAPHK-TMQGTVITLTSPLTGEVKALS</entry><entry>538</entry></row><row><entry /></row><row><entry>Query:</entry><entry>541</entry><entry>QASDPVFSQGIMGKGVVIDPSDGELVSPVDATVSVLFPTKHAIGLLTSEGVEFLIHIGMD</entry><entry>600</entry></row><row><entry /><entry /><entry>+A DPVF+QG+MG+G ++ P++G LV+P DA VSVLFPTKHAI L+T+EG+E L+HIGMD</entry></row><row><entry>Sbjct:</entry><entry>539</entry><entry>EAVDPVFAQGVMGQGALLQPTEGVLVAPCDAEVSVLFPTKHAICLVTTEGLELLMHIGMD</entry><entry>598</entry></row><row><entry /></row><row><entry>Query:</entry><entry>601</entry><entry>TVNLEGKGFTSHVAQGDTVKVGDKLITFDIPMIKEEGYIVETPILITNQQEFRPEELIDL</entry><entry>660</entry></row><row><entry /><entry /><entry>TVNL+G+GF + V QGD VK G  LI FDI  I E GY  ETP+++TNQ  F       L</entry></row><row><entry>Sbjct:</entry><entry>599</entry><entry>TVNLDGQGFEALVKQGDQVKAGQTLIQFDIAAISEAGYATETPLVVTNQDVFTVTVEGSL</entry><entry>658</entry></row><row><entry /></row><row><entry>Query:</entry><entry>661</entry><entry>PKQIKRGQALMVAKK</entry><entry>675</entry></row><row><entry /><entry /><entry>P+QIK    L VA K</entry></row><row><entry>Sbjct:</entry><entry>659</entry><entry>PRQIKVNDKLAVAVK</entry><entry>673</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 146

A DNA sequence (GBSx0052) was identified in <i>S. agalactiae </i>&lt;SEQ ID 487&gt; which encodes the amino acid sequence &lt;SEQ ID 488&gt;. This protein is predicted to be dextran glucosidase DexS (treC). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00504" num="00504"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3493(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00505" num="00505"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB65079 GB: U35633 dextran glucosidase DexS [<i>Streptococcus suis</i>]</entry><entry /></row><row><entry>Identities = 383/547 (70%), Positives = 439/547 (80%), Gaps = 13/547 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLAELGIDMVWLNPFYPSPQRDNG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYL ELGIDM+WLNPFYPSPQRDNG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLKELGIDMIWLNPFYPSPQRDNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YDISDYTAINPDFGTMDDFEEMIEVGRQYRIDFMLDMVLNHCSIEHEWFKKALAGDRYYQ</entry><entry>120</entry></row><row><entry /><entry /><entry>YDISDYTA+NPDFGTM DFEEM+ VG++  I+FMLDMVLNHCS +HEWF+KAL+GD+YYQ</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YDISDYTAVNPDFGTMADFEEMVTVGKELGIEFMLDMVLNHCSTDHEWFQKALSGDQYYQ</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DFFILRDNPTDWVSKFGGNAWAPFGDTGKYYLHLFDITQADLNWRNADVRKELFKVVNFW</entry><entry>180</entry></row><row><entry /><entry /><entry>DFFILRD PTDWVSKFGGNAWAPFGDTGKYYLHLFD+TQADLNWRN  +R+ELFKVVNFW</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>DFFILRDQPTDWVSKFGGNAWAPFGDTGKYYLHLFDVTQADLNWRNPHIREELFKVVNFW</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>RDKGVKGFRFDVINLIGKDEILENCPINDGKPAYTDRPITHDYLKMLNNASFGQDDSFMT</entry><entry>240</entry></row><row><entry /><entry /><entry>+DKGVKGFRFDVINLIGKDE  E+CPINDGKPAYTDRPITHDYLKM+NNA+FG +  FMT</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KDKGVKGFRFDVINLIGKDEAREDCPINDGKPAYTDRPITHDYLKMMNNATFGSEKGFMT</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VGEMSSTTIANCILYTAPEREELSMAFNFHHLKVDYKDGQKWTIMAFDFPALRDLFHSWG</entry><entry>300</entry></row><row><entry /><entry /><entry>VGEMS+TTI NCILYTAPER+ELSMAFNFHHLKVDYKDGQKWTIM FDF  L+ LFH+WG</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>VGEMSATTIENCILYTAPERKELSMAFNFHHLKVDYKDGQKWTIMDFDFEELKHLFHTWG</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>EGMSEGNGWNALFYNNHDQPRALNRFVDVKRFRNEGATMLAASIHLSRGTPYIYMGEEIG</entry><entry>360</entry></row><row><entry /><entry /><entry>E MS GNGWNALFYNNHDQPRALNRF+DV+ FR EGATMLAASIHLSRG</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>EEMSVGNGWNALFYNNHDQPRALNRFIDVENFRKEGATMLAASIHLSRGNNLTST-----</entry><entry>355</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>MLDPDYSSMDDYVDIESLNAYQIMLDEGKSQEEAFSIIRAKSRDNSRVPMQWDDS-----</entry><entry>415</entry></row><row><entry /><entry /><entry> +    SS    +   +   + + +    S  +   + R  SR +   P+</entry></row><row><entry>Sbjct:</entry><entry>356</entry><entry>WVRRSVSSTLTTIAWTTTWTWSLSMPTRCSWTKVTRLSR-PSRLSRPSPVTIPAPRCNGT</entry><entry>414</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>--TNAGFSEGAPWLKVGKSYKEINVAKEKTGLIFTFYQELIRLRKQLPIIADGNYKAAFK</entry><entry>473</entry></row><row><entry /><entry /><entry>  T     +  PWLK GKSY+ INV +EKTG IFTFY+    LRK+LP+I++G+YKAA+K</entry></row><row><entry>Sbjct:</entry><entry>415</entry><entry>LLTMQASQQATPWLKAGKSYQTINVEQEKTGPIFTFYKRTHPLRKELPLISEGDYKAAYK</entry><entry>474</entry></row><row><entry /></row><row><entry>Query:</entry><entry>474</entry><entry>DNEKVYAFERHLDKEKLLVLNNFFAEKVKIKLPENYLQGQVLLSNYKDVTLDETVTLQPY</entry><entry>533</entry></row><row><entry /><entry /><entry>D++KVYAFER L+ EKLLVLNNFFAE+V++ L ++Y  GQVL+SNY D  L + + L+PY</entry></row><row><entry>Sbjct:</entry><entry>475</entry><entry>DSQKVYAFERLLNDEKLLVLNNFFAEEVELDLADDYAHGQVLISNYPDNKLGKKIILKPY</entry><entry>534</entry></row><row><entry /></row><row><entry>Query:</entry><entry>534</entry><entry>QTLAILV</entry><entry>540</entry></row><row><entry /><entry /><entry>Q LAI V</entry></row><row><entry>Sbjct:</entry><entry>535</entry><entry>QALAIQV</entry><entry>541</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 489&gt; which encodes the amino acid sequence &lt;SEQ ID 490&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00506" num="00506"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3631(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00507" num="00507"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 431/539 (79%), Positives = 486/539 (89%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLAELGIDMVWLNPFYPSPQRDNG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTIDK+KVVYQIYPKSYKDTTGNGVGDL GII+KLPYL ELGIDM+WLNPFYPSPQRDNG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTIDKKKVVYQIYPKSYKDTTGNGVGDLLGIIDKLPYLQELGIDMIWLNPFYPSPQRDNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YDISDYTAINPDFGTMDDFEEMIEVGRQYRIDFMLDMVLNHCSIEHEWFKKALAGDRYYQ</entry><entry>120</entry></row><row><entry /><entry /><entry>YD+SDYTA+NPDFGTM DFE +++  ++++I+ MLDMVLNHCS +HEWF+KALAGD YYQ</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YDVSDYTAVNPDFGTMADFENLVKAAKEHQIELMLDMVLNHCSTDHEWFQKALAGDPYYQ</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>DFFILRDNPTDWVSKFGGNAWAPFGDTGKYYLHLFDITQADLNWRNADVRKELFKVVNFW</entry><entry>180</entry></row><row><entry /><entry /><entry>DFFILRD PTDWVSKFGGNAWAPFGDTGKYYLHLFD+TQADLNWRN  VR+EL KVVNFW</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>DFFILRDQPTDWVSKFGGNAWAPFGDTGKYYLHLFDVTQADLNWRNPHVREELAKVVNFW</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>RDKGVKGFRFDVINLIGKDEILENCPINDGKPAYTDRPITHDYLKMLNNASFGQDDSFMT</entry><entry>240</entry></row><row><entry /><entry /><entry>RDKGVKGFRFDVINLIGKDE L +CP+NDGKPAYTDRPITH YL  LN ASFGQDDSFMT</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>RDKGVKGFRFDVINLIGKDEELVDCPVNDGKPAYTDRPITHTYLHDLNQASFGQDDSFMT</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>VGEMSSTTIANCILYTAPEREELSMAFNFHHLKVDYKDGQKWTIMAFDFPALRDLFHSWG</entry><entry>300</entry></row><row><entry /><entry /><entry>VGEMS+TTI NC+LYTAPEREELSMAFNFHHLKVDY++GQKWTIMAFDF ALRDLFH+WG</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>VGEMSATTIDNCLLYTAPEREELSMAFNFHHLKVDYENGQKWTIMAFDFAALRDLFHAWG</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>EGMSEGNGWNALFYNNHDQPRALNRFVDVKRFRNEGATMLAASIHLSRGTPYIYMGEEIG</entry><entry>360</entry></row><row><entry /><entry /><entry>EGMS+GNGWNALFYNNHDQPRALNRFVDV  FRNEGATMLAASIHLSRGTPYIYMGEEIG</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>EGMSQGNGWNALFYNNHDQPRALNRFVDVTHFRNEGATMLAASIHLSRGTPYIYMGEEIG</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>MLDPDYSSMDDYVDIESLNAYQIMLDEGKSQEEAFSIIRAKSRDNSRVPMQWDDSTNAGF</entry><entry>420</entry></row><row><entry /><entry /><entry>MLDPD+ SMDDYVD+ESLNAY  +L  GKS EEAF+II+AKSRDN+R PMQWD S +AGF</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>MLDPDFDSMDDYVDVESLNAYSSLLVSGKSAEEAFAIIKAKSRDNARTPMQWDASEHAGF</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>SEGAPWLKVGKSYKEINVAKEKTGLIFTFYQELIRLRKQLPIIADGNYKAAFKDNEKVYA</entry><entry>480</entry></row><row><entry /><entry /><entry>+ G PWL+VGKSY++INV  EK G IF FYQ LI LRK+LPIIA+G+Y+AAFKD++ VYA</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>TTGKPWLEVGKSYRDINVETEKEGRIFPFYQRLIALRKELPIIAEGDYRAAFKDSQAVYA</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>FERHLDKEKLLVLNNFFAEKVKIKLPENYLQGQVLLSNYKDVTLDETVTLQPYQTLAIL</entry><entry>539</entry></row><row><entry /><entry /><entry>FERHL  + LLVLN+F+A++V+++LP  Y  GQVL+SNY+ V++ E V L+PYQTLAIL</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>FERHLGDQCLLVLNHFYADEVELELPPRYQHGQVLISNYEKVSICEKVILKPYQTLAIL</entry><entry>539</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 147

A DNA sequence (GBSx0153) was identified in <i>S. agalactiae </i>&lt;SEQ ID 491&gt; which encodes the amino acid sequence &lt;SEQ ID 492&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00508" num="00508"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="28pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.03</entry><entry>Transmembrane</entry><entry>8-24 (8-25)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2211(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 148

A DNA sequence (GBSx0154) was identified in <i>S. agalactiae </i>&lt;SEQ ID 493&gt; which encodes the amino acid sequence &lt;SEQ ID 494&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00509" num="00509"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00510" num="00510"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB03939 GB: AP001507 unknown conserved protein</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 190/639 (29%), Positives = 331/639 (51%), Gaps = 34/639 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>TVVIMLVFLARKNLSLYELTVQTKFSIKVIIEQINYLNSFLAKNHLPAIAHSAGRYQLLG</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>T ++  +  AR  L + ELT +   S + +   +  +NS+L +  L A+ +      L+</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>TFILTQLLHARSYLPIQELTQKLNVSRRTVYNDLEKINSWLEEQGLKAV-YKVRSQGLIL</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>DEKEHDKI---VSLLEAEQFYLTQEERVCLIYLYSFCRREFVSNVHYQDFLKVSKNTTLS</entry><entry>122</entry></row><row><entry /><entry /><entry>DE+  ++I   +  L++  +  + +ER   + +Y   R E +   H  D   VS+NTT+</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>DERAKEEIPTKLRSLKSWHYEYSAQERKAWVVIYLLTRLEPLFLEHLMDRTGVSRNTTID</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>DIKMLRSKLAKRGISLTYTRAKGYSLVGDEMDKHQVAFQMITQLLE--------SPIGFW</entry><entry>174</entry></row><row><entry /><entry /><entry>DIK L+ +L    ++L + R  GY++ GDE DK +     ++Q L         SPI  +</entry></row><row><entry>Sbjct:</entry><entry>127</entry><entry>DIKCLKDELNNFHLALEFERKDGYTISGDETDKRKALVYYLSQALPQQNWETELSPIRIF</entry><entry>186</entry></row><row><entry /></row><row><entry>Query:</entry><entry>175</entry><entry>SLNYILSSWKFALSYEKLEKTVEYFYESFQLSPIQ---DRLEKSLYFIILILCRYQRSVD</entry><entry>231</entry></row><row><entry /><entry /><entry>      +   F +  E+L+K  +   ES ++  IQ   D L       +L + R  +</entry></row><row><entry>Sbjct:</entry><entry>187</entry><entry>LRTKRDNGRIFTI--EELQKVYDVISESEKVLKIQYTDDVLHSLSLRFLLFMKRVAKG--</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>232</entry><entry>RVLQGSPIVSEQLK-----ELTTIIVTNLSQDISLSKPLDQKEKDYITLILSGCF-----</entry><entry>281</entry></row><row><entry /><entry /><entry>+ ++  P+  + LK     E   ++   L Q   +  P D++     T ILS</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>KFIKVHPLEKQVLKGTKEYEAAKVMSFKLEQAFGVHYP-DEEVLYLTTHILSSKINYANG</entry><entry>301</entry></row><row><entry /></row><row><entry>Query:</entry><entry>282</entry><entry>EGEGTKDDDFFEALAKAIVDEMETVSLLNFSNKEELLQGLKRHIIPAYFRLKYGLTGDSG</entry><entry>341</entry></row><row><entry /><entry /><entry>E E  K+      +  ++V++ +  + + F  KE L + L  HI PA++R+KYGL  ++</entry></row><row><entry>Sbjct:</entry><entry>302</entry><entry>EIESRKESQELTHIVTSMVNDFQKYACVVFEEKELLEKNLFFHIKPAFYRIKYGLEVENN</entry><entry>361</entry></row><row><entry /></row><row><entry>Query:</entry><entry>342</entry><entry>YTQNIKEHYSDLFLLVKKALRPLEEQVGL-IPDSEISYFVIHFGGYLRQSGGTQSMSYKA</entry><entry>400</entry></row><row><entry /><entry /><entry>  ++IK  Y +LFLL +K +  LE  VG  + D+E+++  +HF G++R+ G   +   KA</entry></row><row><entry>Sbjct:</entry><entry>362</entry><entry>IAESIKTSYPELFLLTRKVVHYLERYVGKSVNDNEVAFITMHFVGWMRREGTIPTKRKKA</entry><entry>421</entry></row><row><entry /></row><row><entry>Query:</entry><entry>401</entry><entry>LILCPNGVSSSLVIKEKLRGLFPQIHFHRVSKIEQLKLIDNQTYDMVFSTIFVETKKPNY</entry><entry>460</entry></row><row><entry /><entry /><entry>LI+C NGV +S  +K +L GLFP +   +   I + +    +   ++ +T   E   P +</entry></row><row><entry>Sbjct:</entry><entry>422</entry><entry>LIVCANGVGTSQFLKNQLEGLFPAVDIIKTCSIREYEKTPVEVDFIISTTSIPEKNVPIF</entry><entry>481</entry></row><row><entry /></row><row><entry>Query:</entry><entry>461</entry><entry>LVSLMMT-AEQVQQLKELVISDFPKACLDDFQLDQLIATIKKYAHVHCEEELKLALRTMV</entry><entry>519</entry></row><row><entry /><entry /><entry>+V+ ++T  E+ + LK + ++      +  + ++ L+  IK++ +V  E+ L   LR</entry></row><row><entry>Sbjct:</entry><entry>482</entry><entry>IVNPILTETEKERLLKSVHVALDELGAMKGYSIEGLMDVIKRHGNVDDEKALYQDLRRFF</entry><entry>541</entry></row><row><entry /></row><row><entry>Query:</entry><entry>520</entry><entry>KQD--ILRKDVRPLLHQLITEETYQTSSEQMNWKEAIRLAAKPLLASGKITESYPEAMIE</entry><entry>577</entry></row><row><entry /><entry /><entry> Q   I  K  +P L+QL+TE+  Q   +  +W+EAI+LAAKPLL  G +TESY + MI+</entry></row><row><entry>Sbjct:</entry><entry>542</entry><entry>TQPTPIGPKQEKPDLNQLLTEDMIQLREQVTHWQEAIQLAAKPLLLKGMVTESYVKKMIK</entry><entry>601</entry></row><row><entry /></row><row><entry>Query:</entry><entry>578</entry><entry>KVEEFGPFINLGKGIAIPHARPEDGVNSVGMSMLVLEQP</entry><entry>616</entry></row><row><entry /><entry /><entry> +E+FGP++ +    AIPHA+PEDGV  +GMS+L L++P</entry></row><row><entry>Sbjct:</entry><entry>602</entry><entry>NIEKFGPYMIIAPHFAIPHAKPEDGVRQLGMSLLWLKKP</entry><entry>640</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 495&gt; which encodes the amino acid sequence &lt;SEQ ID 496&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00511" num="00511"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57 or 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.64</entry><entry>Transmembrane</entry><entry>123-139 (123-139)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1256(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00512" num="00512"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 187/624 (29%), Positives = 327/624 (51%), Gaps = 20/624 (3%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVDNKTVVIMLVFLARKNLSLYELTVQTKFSIKVIIEQINYLNSFLAKNHLPAIAHSAGR</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+ ++ +    +F   K  SL       K S + I+  I  +N  L+   LP IA</entry></row><row><entry>Sbjct:</entry><entry>35</entry><entry>MLSHELIRNYQLFSKYKGHSLEAFESILKASKRHILADIAKINDTLSLYQLPLIALDR--</entry><entry>92</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YQLL--GDEKEHDKIVSLLEAEQFYLTQEERVCLIYLYSFCRREFVSNVHYQDFLKVSKN</entry><entry>118</entry></row><row><entry /><entry /><entry> QL+   D  E D +  +L     YL Q+ER+ +I +Y    +EF+S  H +  L++S+N</entry></row><row><entry>Sbjct:</entry><entry>93</entry><entry>-QLVYPPDLTEKDLLNRMLPTLDDYLFQDERLDMIIIYIMMAKEFISINHLESLLRLSRN</entry><entry>151</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>TTLSDIKMLRSKLAKRGISLTYTRAKGYSLVGDEMDKHQVAFQMITQLLESPIGFWSLNY</entry><entry>178</entry></row><row><entry /><entry /><entry>+ ++D+ ++R ++    ++L Y R  GY   G+ +   ++    ++ LL+   G W  +Y</entry></row><row><entry>Sbjct:</entry><entry>152</entry><entry>SVIADLNLVRDRVQAFQVTLAYNRQDGYFFEGEPLALRRLLESAVSSLLQVTSGPWVFSY</entry><entry>211</entry></row><row><entry /></row><row><entry>Query:</entry><entry>179</entry><entry>ILSSWKFALSYEKLEKTVEYFYESFQLSPIQDRLEKSLYFIILILCR-YQRSVD-RVLQG</entry><entry>236</entry></row><row><entry /><entry /><entry>+L         + +  T+E       L+ I ++L   +YF  L+  R + R+V    +</entry></row><row><entry>Sbjct:</entry><entry>212</entry><entry>LLHELGLPDQKKVMAATLEELSRENHLTFISEKLRDLIYFFCLLAHRPFSRNVRAEAVDT</entry><entry>271</entry></row><row><entry /></row><row><entry>Query:</entry><entry>237</entry><entry>SPIVSEQLKELTTIIVTNLSQDISLSKPLDQKEKDYITLILSGCFEG--EGTKDDDFFEA</entry><entry>294</entry></row><row><entry /><entry /><entry> P+ S  ++ +   ++ N         P   +EK  +   L GC +G  E       ++</entry></row><row><entry>Sbjct:</entry><entry>272</entry><entry>FPLASPAVETMVDQLLVNF--------PSLTEEKYLVQSRLLGCIQGDLELVFQQPIYDI</entry><entry>323</entry></row><row><entry /></row><row><entry>Query:</entry><entry>295</entry><entry>LAKAIVDEMETVSLLNFSNKEELLQGLKRHIIPAYFRLKYGLTGDSGYTQNIKEHYSDLF</entry><entry>354</entry></row><row><entry /><entry /><entry>+ + I++ +   + L+ ++  EL Q L  H++PAY+RL Y +   +   + IK+ Y  LF</entry></row><row><entry>Sbjct:</entry><entry>324</entry><entry>MEE-IINSVAVNTGLSITDTPELRQNLYSHLLPAYYRLYYDINLTNPLKEQIKQDYESLF</entry><entry>382</entry></row><row><entry /></row><row><entry>Query:</entry><entry>355</entry><entry>LLVKKALRPLEEQVGL-IPDSEISYFVIHFGGYLRQSGGTQSMSYKALILCPNGVSSSLV</entry><entry>413</entry></row><row><entry /><entry /><entry> LVK++L PLE+Q+G  + + E++YF IHFG +L+      S    AL +CPNG+SSSL+</entry></row><row><entry>Sbjct:</entry><entry>383</entry><entry>YLVKRSLSPLEKQLGKSVNEDEVAYFTIHFGRWLQAPKKRPSNQLVALSVCPNGISSSLM</entry><entry>442</entry></row><row><entry /></row><row><entry>Query:</entry><entry>414</entry><entry>IKEKLRGLFPQIHFHRVSKIEQLKLIDNQTYDMVFSTIFVETKKPNYLVSLMMTAEQVQQ</entry><entry>473</entry></row><row><entry /><entry /><entry>++  L+ LFPQ+ F R+ +++++KL+D  ++D++FST+  +  KP Y+   +M   +</entry></row><row><entry>Sbjct:</entry><entry>443</entry><entry>LEATLKELFPQLQFIRIHQLDKIKLLDPASFDLIFSTVAFDCAKPVYVTQALMGPVEKMM</entry><entry>502</entry></row><row><entry /></row><row><entry>Query:</entry><entry>474</entry><entry>LKELVISDFPKACLDDFQLDQLIATIKKYAHVHCEEELKLAL-RTMVKQDILRKDVRPLL</entry><entry>532</entry></row><row><entry /><entry /><entry>LK++V  DF     + F LD L++ I K+  +  +E L   L R ++   +  +     L</entry></row><row><entry>Sbjct:</entry><entry>503</entry><entry>LKKMVCDDFHLPLSEQFALDDLLSIIHKHTTITNKEGLVSDLSRYLIGNHLTIEKGGLGL</entry><entry>562</entry></row><row><entry /></row><row><entry>Query:</entry><entry>533</entry><entry>HQLITEETYQTSSEQMNWKEAIRLAAKPLLASGKITESYPEAMIEKVEEFGPFINLGKGI</entry><entry>592</entry></row><row><entry /><entry /><entry>  L+T +  + +    +W+EAIRLAA+PLL    I  SY + MI+ V E G +I L   +</entry></row><row><entry>Sbjct:</entry><entry>563</entry><entry>LDLLTADFIRQADAVSDWQEAIRLAAQPLLEHQMIETSYIDGMIDSVNELGAYIVLAPKV</entry><entry>622</entry></row><row><entry /></row><row><entry>Query:</entry><entry>593</entry><entry>AIPHARPEDGVNSVGMSMLVLEQP</entry><entry>616</entry></row><row><entry /><entry /><entry>A+PHA PE G   +GMS+L L++P</entry></row><row><entry>Sbjct:</entry><entry>623</entry><entry>AVPHAAPEKGTRQLGMSLLQLKEP</entry><entry>646</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 149

A DNA sequence (GBSx0155) was identified in <i>S. agalactiae </i>&lt;SEQ ID 497&gt; which encodes the amino acid sequence &lt;SEQ ID 498&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00513" num="00513"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3665(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 499&gt; which encodes the amino acid sequence &lt;SEQ ID 500&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00514" num="00514"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3665(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00515" num="00515"><table frame="none" colsep="0" rowsep="0" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="217pt" align="left" /><colspec colname="2" colwidth="0pt" align="left" /><tbody valign="top"><row><entry>Identities = 33/35 (94%), Positives = 35/35 (99%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="center" /><colspec colname="3" colwidth="154pt" align="left" /><colspec colname="4" colwidth="21pt" align="center" /><colspec colname="5" colwidth="0pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEKEAKQIIDLKRNLFKIDVRAQKDEEKVFMRTAW</entry><entry>35</entry><entry /></row><row><entry /><entry /><entry>+EKEAKQ+IDLKRNLFKIDVRAQKDEEKVFMRTAW</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LEKEAKQMIDLKRNLFKIDVRAQKDEEKVFMRTAW</entry><entry>35</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 150

A repeated DNA sequence (GBSx0156) was identified in <i>S. agalactiae </i>&lt;SEQ ID 501&gt; which encodes the amino acid sequence &lt;SEQ ID 502&gt;. This protein is predicted to be a repeat-associated protein in rhsc-phrb intergenic region. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00516" num="00516"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane</entry><entry>29-45 (28-48)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2826(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A closely-related DNA sequence was identified in <i>S. agalactiae </i>&lt;SEQ ID 1035&gt; which encodes the amino acid sequence &lt;SEQ ID 1036&gt;. Further related GBS sequences are: &lt;SEQ ID 9067&gt;, &lt;SEQ ID 9068&gt;, &lt;SEQ ID 9497&gt;, &lt;SEQ ID 9498&gt;, &lt;SEQ ID 9733&gt;, &lt;SEQ ID 9734&gt;

A related repeated DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 503&gt; which encodes the amino acid sequence &lt;SEQ ID 504&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00517" num="00517"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="28pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane</entry><entry>29-45 (28-48)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2826(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8547&gt; and protein &lt;SEQ ID 8548&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00518" num="00518"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop Possible site: −1 Crend: 5</entry><entry /></row><row><entry>McG: Discrim Score: −7.73</entry></row><row><entry>GvH: Signal Score (−7.5): −3.88</entry></row><row><entry>     Possible site: 44</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 1 value: −4.57 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="70pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane</entry><entry>26-42 (25-45)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 2.12</entry><entry>334</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 1.41</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.2826(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 7071&gt; which encodes the amino acid sequence &lt;SEQ ID 7072&gt;. An alignment of the GAS and GBS sequences follows:

<tables id="TABLE-US-00519" num="00519"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Score = 767 bits (1960), Expect = 0.0</entry><entry /></row><row><entry>Identities = 375/377 (99%), Positives = 375/377 (99%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>MIDFIISIDDCAVELDSRQSWKIRSPLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>MIDFIISIDDCAVELDSRQSWKIR PLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MIDFIISIDDCAVELDSRQSWKIRYPLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>TYVDLSEGCSSHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG</entry><entry>123</entry></row><row><entry /><entry /><entry>TYVDLSEGC SHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TYVDLSEGCPSHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI</entry><entry>183</entry></row><row><entry /><entry /><entry>KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>184</entry><entry>VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE</entry><entry>243</entry></row><row><entry /><entry /><entry>VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>244</entry><entry>YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG</entry><entry>303</entry></row><row><entry /><entry /><entry>YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>304</entry><entry>HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY</entry><entry>363</entry></row><row><entry /><entry /><entry>HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>364</entry><entry>ISVHLEDYLVQLFGERG</entry><entry>380</entry></row><row><entry /><entry /><entry>ISVHLEDYLVQLFGERG</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>ISVHLEDYLVQLFGERG</entry><entry>377</entry></row></tbody></tgroup></table></tables>

A further related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 9087&gt; which encodes the amino acid sequence &lt;SEQ ID 9088&gt;. A further related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 9089&gt; which encodes the amino acid sequence &lt;SEQ ID 9090&gt;. The GAS and GBS proteins are 100% identical.

There is also homology to SEQ IDs 7018 and 8548.

SEQ ID 8548 (GBS318) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 46</figref> (lane 5; MW 70 kDa).

GBS318-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 203</figref>, lane 3.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 151

A DNA sequence (GBSx0157) was identified in <i>S. agalactiae </i>&lt;SEQ ID 505&gt; which encodes the amino acid sequence &lt;SEQ ID 506&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00520" num="00520"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 34</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 496.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 152

A repeated DNA sequence (GBSx0158) was identified in <i>S. agalactiae </i>&lt;SEQ ID 507&gt; which encodes the amino acid sequence &lt;SEQ ID 508&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00521" num="00521"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1054(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00522" num="00522"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB03941 GB: AP001507 unknown conserved protein [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 26/82 (31%), Positives = 52/82 (62%), Gaps = 2/82 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>LRIGTACGSGLGSSFMVQMNIESILKDLGVSDVEVEHYDLGGADPSAADVWIVGRDLEDS</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>++I   CG G G+S +++MN+E++L  LG++  +V++ D+  A    +D  I  ++L +S</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKILCVCGLGQGTSLILKMNVETVLSQLGIA-ADVDNTDVSSASSEQSDFIITSKELAES</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>-AGHLGDVRILNSIIDMDELRE</entry><entry>82</entry></row><row><entry /><entry /><entry> A H   + I+N+  DM+E+++</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>LASHPSKIVIVNNYFDMEEIKQ</entry><entry>81</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 509&gt; which encodes the amino acid sequence &lt;SEQ ID 510&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00523" num="00523"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00524" num="00524"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 27/90 (30%), Positives = 51/90 (56%), Gaps = 1/90 (1%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MLRIGTACGSGLGSSFMVQMNIESILKDLGVSDVEVEHYDLGGADPSAADVWIVGRDLED</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M++I T CG+G+GSS +++M +E+I   LG+ DV+ E  D   A    AD+++  ++ +D</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>MIKIVTVCGNGIGSSLLLRMKVEAIASSLGI-DVDAESCDSNAAVGKGADLFVTVKEFKD</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>SAGHLGDVRILNSIIDMDELRELVTGICQE</entry><entry>90</entry></row><row><entry /><entry /><entry>       V I+ S  +  ++ E +  + +E</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>IFPEDAKVCIVKSYTNRKKIEEDLVPVLKE</entry><entry>96</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 153

A DNA sequence (GBSx0159) was identified in <i>S. agalactiae </i>&lt;SEQ ID 511&gt; which encodes the amino acid sequence &lt;SEQ ID 512&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00525" num="00525"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 154

A DNA sequence (GBSx0160) was identified in <i>S. agalactiae </i>&lt;SEQ ID 513&gt; which encodes the amino acid sequence &lt;SEQ ID 514&gt;. This protein is predicted to be sgaT. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00526" num="00526"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 16</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −14.97</entry><entry>Transmembrane</entry><entry>424-440 (411-447)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.86</entry><entry>Transmembrane</entry><entry>224-240 (221-248)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.27</entry><entry>Transmembrane</entry><entry>134-150 (124-167)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.11</entry><entry>Transmembrane</entry><entry>321-337 (314-349)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.64</entry><entry>Transmembrane</entry><entry>379-395 (370-397)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.21</entry><entry>Transmembrane</entry><entry> 96-112 (94-115)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.05</entry><entry>Transmembrane</entry><entry>267-283 (257-289)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.13</entry><entry>Transmembrane</entry><entry>  18-34 (17-35)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.55</entry><entry>Transmembrane</entry><entry>151-167 (151-167)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.32</entry><entry>Transmembrane</entry><entry>  42-58 (42-58)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6986(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00527" num="00527"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB52363 GB: AL109747 putative integral membrane protein</entry><entry /></row><row><entry>[<i>Streptomyces coelicolor </i>A3(2)]</entry></row><row><entry>Identities = 202/453 (44%), Positives = 292/453 (63%), Gaps = 22/453 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>FLVN-IASTPAILVALIAIIGLVLQKKGVPDIVKGGIKTFVGFLVVSGGTGIVQNSLNPF</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>FLVN I S PA L+ +I  +GL   KK V   V G IK  +G L+V  G G+V +SL+P</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>FLVNEILSQPAYLIGIITAVGLAALKKSVGQTVGGAIKATLGLLLVGAGAGLVSSSLDPL</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>GKMFEHAFHLVGVVPNNEAIVAVALTKYGSATALIMLAGMIFNILIARFTKFKYIFLTGH</entry><entry>125</entry></row><row><entry /><entry /><entry>G+M +      GV+P NEAIV +A +++G+  A +M+ G + ++ +ARFT  +Y+FLTGH</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>GRMIQGTTGTHGVIPTNEAIVGIAQSEFGARVAWLMILGFLVSLALARFTPLRYVFLTGH</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>HTLYMACMIAVIFAVAGFTSFSLILFGGLALGIIMSVSPAFVQKYMIQLTGNDKVALGHF</entry><entry>185</entry></row><row><entry /><entry /><entry>H L+MA ++ ++ A AG  S +++L GG+ +GI++   PAF   +  ++TGND +A+GHF</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>HMLFMATLLTIVMATAGQGSVAVVLGGGVLVGILLVALPAFAHPWTKKVTGNDTLAIGHF</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>GSLGYWLSGFIGGIVGDKSKSTEDIKFPKSLSFLRDSTVSITISMAIIYLIVAV------</entry><entry>239</entry></row><row><entry /><entry /><entry>G+ GY +SG  G +VG  S+STE++K P+ L FLRDS V+  +SM +IYL++++</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>GTAGYIVSGATGQLVGKNSRSTEEMKLPEGLRFLRDSMVATALSMVLIYLVMSLLFLAKV</entry><entry>249</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>--------FAGEAYIAKEISNGVNGLVYALQLAGQFAAGVFVILAGVRLILGEIVPAFKG</entry><entry>291</entry></row><row><entry /><entry /><entry>        FAG        ++  N L+ ++    QF  GV VIL GVR ILGE+VPAF+G</entry></row><row><entry>Sbjct:</entry><entry>250</entry><entry>GQDAAFKAFAGSG--GDPAADVGNYLMQSVMQGLQFGIGVAVILFGVRTILGELVPAFQG</entry><entry>307</entry></row><row><entry /></row><row><entry>Query:</entry><entry>292</entry><entry>ISEKLVPNSKPALDCPIVYPYAPNAVLIGFISSFVGGLVSMIVMI-----VTGTTVILPG</entry><entry>346</entry></row><row><entry /><entry /><entry>I+ ++VP +KPALD PIV+PYA NAVLIGFI SF+GGL  +  +I       G  ++LPG</entry></row><row><entry>Sbjct:</entry><entry>308</entry><entry>IAGRVVPGAKPALDAPIVFPYAQNAVLIGFIFSFLGGLTGLAALIWVFNPAFGLALVLPG</entry><entry>367</entry></row><row><entry /></row><row><entry>Query:</entry><entry>347</entry><entry>VVPHFFCGATAGVIGNASGGVRGATIGAFVQGILISFLPIFLMPVLGGLGFKGSTFSDAD</entry><entry>406</entry></row><row><entry /><entry /><entry>+VPHFF G  AGV GNA+GG RGA +G+F+ G+LI+FLP  L+  LG  G   +TF DAD</entry></row><row><entry>Sbjct:</entry><entry>368</entry><entry>LVPHFFTGGAAGVYGNATGGRRGAAVGSFLNGLLITFLPAILLKALGSFGEANTTFGDAD</entry><entry>427</entry></row><row><entry /></row><row><entry>Query:</entry><entry>407</entry><entry>FGLTGIILGALNHVGGAIAIVIGIVVILIGLFG</entry><entry>439</entry></row><row><entry /><entry /><entry>FG  G +LG++  + G   ++  ++  L+ L G</entry></row><row><entry>Sbjct:</entry><entry>428</entry><entry>FGWFGAVLGSIGKLDGTAGLIGMLIFGLLILAG</entry><entry>460</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 515&gt; which encodes the amino acid sequence &lt;SEQ ID 516&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00528" num="00528"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 34</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.33</entry><entry>Transmembrane</entry><entry>330-346 (315-353)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.17</entry><entry>Transmembrane</entry><entry>227-243 (221-246)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.62</entry><entry>Transmembrane</entry><entry>127-143 (126-145)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.25</entry><entry>Transmembrane</entry><entry>269-285 (266-291)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry>  43-59 (41-62)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.66</entry><entry>Transmembrane</entry><entry> 98-114 (91-116)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.76</entry><entry>Transmembrane</entry><entry>146-162 (145-163)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.59</entry><entry>Transmembrane</entry><entry>308-324 (308-324)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4333(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00529" num="00529"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB52363 GB: AL109747 putative integral membrane protein</entry><entry /></row><row><entry>[<i>Streptomyces coelicolor </i>A3(2)]</entry></row><row><entry>Identities = 162/387 (41%), Positives = 245/387 (62%), Gaps = 17/387 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>IRDILKEPAFLMGLIAFAGLVALKTPAHKVLTGTLGPILGYLMLVAGAGVIVTNLDPLAK</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>+ +IL +PA+L+G+I   GL ALK    + + G +   LG L++ AGAG++ ++LDPL +</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>VNEILSQPAYLIGIITAVGLAALKKSVGQTVGGAIKATLGLLLVGAGAGLVSSSLDPLGR</entry><entry>71</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>LIEHGFSITGVVPNNEAVTSVAQKILGVETMSILVVGLLLNLAFARFTRFKYIFLTGHHS</entry><entry>127</entry></row><row><entry /><entry /><entry>+I+      GV+P NEA+  +AQ   G     ++++G L++LA ARFT  +Y+FLTGHH</entry></row><row><entry>Sbjct:</entry><entry>72</entry><entry>MIQGTTGTHGVIPTNEAIVGIAQSEFGARVAWLMILGFLVSLALARFTPLRYVFLTGHHM</entry><entry>131</entry></row><row><entry /></row><row><entry>Query:</entry><entry>128</entry><entry>FFMACLLSAVLGAVGFKGSLLIIL-DGFLLGAWSAISPAIGQQYTLKVTDGDEIAMGHFG</entry><entry>186</entry></row><row><entry /><entry /><entry> FMA LL+ V+   G +GS+ ++L  G L+G      PA    +T KVT  D +A+GHFG</entry></row><row><entry>Sbjct:</entry><entry>132</entry><entry>LFMATLLTIVMATAG-QGSVAVVLGGGVLVGILLVALPAFAHPWTKKVTGNDTLAIGHFG</entry><entry>190</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>SLGYYLSAWVGSKVGKDSKDTEDLQISEKWSFLRNTTISTGLIMVIFYLVAT---VASVL</entry><entry>243</entry></row><row><entry /><entry /><entry>+ GY +S   G  VGK+S+ TE++++ E   FLR++ ++T L MV+ YLV +   +A V</entry></row><row><entry>Sbjct:</entry><entry>191</entry><entry>TAGYIVSGATGQLVGKNSRSTEEMKLPEGLRFLRDSMVATALSMVLIYLVMSLLFLAKVG</entry><entry>250</entry></row><row><entry /></row><row><entry>Query:</entry><entry>244</entry><entry>RNASVAEELAAGQNP-------FIFAIKSGLTFAVGVAIVYAGVRMILADLIPAFQGIAN</entry><entry>296</entry></row><row><entry /><entry /><entry>++A+      +G +P        + ++  GL F +GVA++  GVR IL +L+PAFQGIA</entry></row><row><entry>Sbjct:</entry><entry>251</entry><entry>QDAAFKAFAGSGGDPAADVGNYLMQSVMQGLQFGIGVAVILFGVRTILGELVPAFQGIAG</entry><entry>310</entry></row><row><entry /></row><row><entry>Query:</entry><entry>297</entry><entry>KLIPNAIPAVDCAVFFPYAPTAVIIGFASSFVGGLLGMLIL-----GVAGGVLIIPGMVP</entry><entry>351</entry></row><row><entry /><entry /><entry>+++P A PA+D  + FPYA  AV+IGF  SF+GGL G+  L        G  L++PG+VP</entry></row><row><entry>Sbjct:</entry><entry>311</entry><entry>RVVPGAKPALDAPIVFPYAQNAVLIGFIFSFLGGLTGLAALIWVFNPAFGLALVLPGLVP</entry><entry>370</entry></row><row><entry /></row><row><entry>Query:</entry><entry>352</entry><entry>HFFCGATAEIFGNSTGGRRGAMIGASL</entry><entry>378</entry></row><row><entry /><entry /><entry>HFF G  A ++GN+TGGRRGA +G+ L</entry></row><row><entry>Sbjct:</entry><entry>371</entry><entry>HFFTGGAAGVYGNATGGRRGAAVGSFL</entry><entry>397</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00530" num="00530"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 174/376 (46%), Positives = 258/376 (68%), Gaps = 2/376 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKGLLDFLVNIASTPAILVALIAIIGLVLQKKGVPDIVKGGIKTFVGFLVVSGGTGIVQN</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+ LL F+ +I   PA L+ LIA  GLV  K     ++ G +   +G+L++  G G++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MEALLSFIRDILKEPAFLMGLIAFAGLVALKTPAHKVLTGTLGPILGYLMLVAGAGVIVT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>SLNPFGKMFEHAFHLVGVVPNNEAIVAVALTKYGSATALIMLAGMIFNILIARFTKFKYI</entry><entry>120</entry></row><row><entry /><entry /><entry>+L+P  K+ EH F + GVVPNNEA+ +VA    G  T  I++ G++ N+  ARFT+FKYI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>NLDPLAKLIEHGFSITGVVPNNEAVTSVAQKILGVETMSILVVGLLLNLAFARFTRFKYI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>FLTGHHTLYMACMIAVIFAVAGFTSFSLILFGGLALGIIMSVSPAFVQKYMIQLTGNDKV</entry><entry>180</entry></row><row><entry /><entry /><entry>FLTGHH+ +MAC+++ +    GF    LI+  G  LG   ++SPA  Q+Y +++T  D++</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>FLTGHHSFFMACLLSAVLGAVGFKGSLLIILDGFLLGAWSAISPAIGQQYTLKVTDGDEI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>ALGHFGSLGYWLSGFIGGIVGDKSKSTEDIKFPKSLSFLRDSTVSITISMAIIYLI--VA</entry><entry>238</entry></row><row><entry /><entry /><entry>A+GHFGSLGY+LS ++G  VG  SK TED++  +  SFLR++T+S  + M I YL+  VA</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>AMGHFGSLGYYLSAWVGSKVGKDSKDTEDLQISEKWSFLRNTTISTGLIMVIFYLVATVA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>239</entry><entry>VFAGEAYIAKEISNGVNGLVYALQLAGQFAAGVFVILAGVRLILGEIVPAFKGISEKLVP</entry><entry>298</entry></row><row><entry /><entry /><entry>     A +A+E++ G N  ++A++    FA GV ++ AGVR+IL +++PAF+GI+ KL+P</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>SVLRNASVAEELAAGQNPFIFAIKSGLTFAVGVAIVYAGVRMILADLIPAFQGIANKLIP</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>299</entry><entry>NSKPALDCPIVYPYAPNAVLIGFISSFVGGLVSMIVMIVTGTTVILPGVVPHFFCGATAG</entry><entry>358</entry></row><row><entry /><entry /><entry>N+ PA+DC + +PYAP AV+IGF SSFVGGL+ M+++ V G  +I+PG+VPHFFCGATA</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>NAIPAVDCAVFFPYAPTAVIIGFASSFVGGLLGMLILGVAGGVLIIPGMVPHFFCGATAE</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>359</entry><entry>VIGNASGGVRGATIGA</entry><entry>374</entry></row><row><entry /><entry /><entry>+ GN++GG RGA IGA</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>IFGNSTGGRRGAMIGA</entry><entry>376</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 155

A DNA sequence (GBSx0161) was identified in <i>S. agalactiae </i>&lt;SEQ ID 517&gt; which encodes the amino acid sequence &lt;SEQ ID 518&gt;. This protein is predicted to be transketolase, N-terminal subunit (tkt). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00531" num="00531"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3680(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00532" num="00532"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB98676 GB: U67515 transketolase' [<i>Methanococcus jannaschii</i>]</entry><entry /></row><row><entry>Identities = 106/269 (39%), Positives = 158/269 (58%), Gaps = 4/269 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>LRRFATEIRLNTLETLNHLGFGHYGGSLSIVEALAVLYGDIMDINPEKFKESDRDYMVLS</entry><entry>70</entry><entry /></row><row><entry /><entry /><entry>L + A ++R N ++ +     GH GGSLS  + +  LY  +M+ +P+   + DRD  VLS</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>LEKIAKKVRYNIVKMVGLAKSGHPGGSLSATDIIVALYFKLMNYSPDNPYKKDRDRFVLS</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>71</entry><entry>KGHAGPALYSTLYLKGFFDKTFLHSLNTNGTKLPSHPDRNLTPGIDVTTGSLGQGISIAT</entry><entry>130</entry></row><row><entry /><entry /><entry>KGHA PALY+ L   G  ++  L  L     KL  HP  + TPG+++ TGSLGQG S A</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>KGHAAPALYAVLSELGIIEEEELWKLRRLEGKLQGHPSMD-TPGVEICTGSLGQGFSAAV</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>131</entry><entry>GIAYAQKIENSSYYTYTIVGDGELNEGQCWEAIQFAAHHQLHHLIVFVDDNKKQLDGLTA</entry><entry>190</entry></row><row><entry /><entry /><entry>G+A   +++  + Y Y ++GDGE  EG  WEA   AAH++L +LI F+D NK Q+DG T</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>GMALGCRLDKLNNYVYVLLGDGECQEGIVWEAAMAAAHYKLDNLIAFIDRNKLQIDGCTE</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>191</entry><entry>DICNPGDFVAKFEAFGFDAVRVKGDDIEAIDKAIKTFQDSNSVRPKCIVLDSIKGQGVKE</entry><entry>250</entry></row><row><entry /><entry /><entry>D+ + GD  AKFEAFG+D   + G + E I   ++  +   + +PK I+  ++KG+GV</entry></row><row><entry>Sbjct:</entry><entry>189</entry><entry>DVMSLGDIKAKFEAFGWDVFEIDGHNFEEIINTVEKAKSMKNGKPKMIIAYTVKGKGVSF</entry><entry>248</entry></row><row><entry /></row><row><entry>Query:</entry><entry>251</entry><entry>LEELASNHHLRPDLQQKTMLERALISLRE</entry><entry>279</entry></row><row><entry /><entry /><entry>+E   + H   P+ +Q   L++AL  L E</entry></row><row><entry>Sbjct:</entry><entry>249</entry><entry>MENNVAFHGKAPNEEQ---LKQALEELSE</entry><entry>274</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 519&gt; which encodes the amino acid sequence &lt;SEQ ID 520&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00533" num="00533"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 26</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.75</entry><entry>Transmembrane</entry><entry>58-74 (57-74)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1298(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related sequence was also identified in GAS &lt;SEQ ID 9165&gt; which encodes the amino acid sequence &lt;SEQ ID 9166&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00534" num="00534"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.75</entry><entry>Transmembrane</entry><entry>40-56 (39-56)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.130(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00535" num="00535"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 82/246 (33%), Positives = 129/246 (52%), Gaps = 15/246 (6%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>18</entry><entry>IRLNTLETLNHLGFGHYGGSLSIVEALAVLYGDIMDINPEKFKE-SDRDYMVLSKGHAGP</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>+R  +++ +     GH G  +       VL+   M+INP+  +  S+RD  +LS GH</entry></row><row><entry>Sbjct:</entry><entry>82</entry><entry>VRTLSMDAIQAANSGHPGLPMGAAPMAYVLWNHFMNINPKTSRNWSNRDRFILSAGHGSA</entry><entry>141</entry></row><row><entry /></row><row><entry>Query:</entry><entry>77</entry><entry>ALYSTLYLKGF-FDKTFLHSLNTNGTKLPSHPDRNLTPGIDVTTGSLGQGISIATGIAYA</entry><entry>135</entry></row><row><entry /><entry /><entry> LYS L+L G+      L +    G+K P HP+ N T G++ TTG LGQGI+ A G+A A</entry></row><row><entry>Sbjct:</entry><entry>142</entry><entry>MLYSLLHLAGYDLSVEDLKNFRQWGSKTPGHPEVNHTDGVEATTGPLGQGIANAVGMAMA</entry><entry>201</entry></row><row><entry /></row><row><entry>Query:</entry><entry>136</entry><entry>QK----------IENSSYYTYTIVGDGELNEGQCWEAIQFAAHHQLHHLIVFVDDNKKQL</entry><entry>185</entry></row><row><entry /><entry /><entry>+            +   +YT+ + GDG+L EG   EA   A H +L  L++  D N   L</entry></row><row><entry>Sbjct:</entry><entry>202</entry><entry>EAHLAAKFNKPGFDIVDHYTFALNGDGDLMEGVSQEAASMAGHLKLGKLVLLYDSNDISL</entry><entry>261</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>DGLTADICNPGDFVAKFEAFGFDAVRVK-GDDIEAIDKAIKTFQDSNSVRPKCIVLDSIK</entry><entry>244</entry></row><row><entry /><entry /><entry>DG T+ +    D   +FEA+G+  + VK G+D+E I  AI+  + + + +P  I + +I</entry></row><row><entry>Sbjct:</entry><entry>262</entry><entry>DGPTS-MAFTEDVKGRFEAYGWQHILVKDGNDLEEIAAAIEAAK-AETEKPTIIEVKTII</entry><entry>319</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>GQGVKE</entry><entry>250</entry></row><row><entry /><entry /><entry>G G ++</entry></row><row><entry>Sbjct:</entry><entry>320</entry><entry>GFGAEK</entry><entry>325</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 156

A DNA sequence (GBSx0162) was identified in <i>S. agalactiae </i>&lt;SEQ ID 521&gt; which encodes the amino acid sequence &lt;SEQ ID 522&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00536" num="00536"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −0.27</entry><entry>Transmembrane</entry><entry>53-69 (53-69)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.1107 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9499&gt; which encodes amino acid sequence &lt;SEQ ID 9500&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00537" num="00537"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB98674 GB: U67515 transketolase‘’ [<i>Methanococcus jannaschii</i>]</entry><entry /></row><row><entry>Identities = 100/301 (33%), Positives = 171/301 (56%), Gaps = 7/301 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>KEMRLVYRDFLLQANQENKQITVLEADLSSSMSTNALASEFGKRYINLGIMEAEMVGLAA</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>K MR  Y + L++  ++ + + VL+ADLS S  T   A EF +R+ N G+ E  M+G+AA</entry></row><row><entry>Sbjct:</entry><entry>9</entry><entry>KGMRKGYGETLIELGKKYENLVVLDADLSGSTQTAMFAKEFPERFFNAGVAEQNMIGMAA</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>GLAIKGYKPYLHTFGPFASRRVFDQVFLSLGYSQLSATIIGSDAGISAEMNGGTHMPFEE</entry><entry>125</entry></row><row><entry /><entry /><entry>GLA  G   +  +F  FAS R ++ +   + Y +L+  I+ + AGI+   +G +H   E+</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>GLATTGKIVFASSFSMFASGRAWEIIRNLVAYPKLNVKIVATHAGITVGEDGASHQMCED</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>LGLLRLIPKATIFEVSDDIQFEAILKQTLSIDGLKYIRTIRKAPTAVYEGRE----DFSK</entry><entry>181</entry></row><row><entry /><entry /><entry>+ ++R IP   +   +D    + +++      G  Y+R  R+    +YE  E    +  K</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>IAIMRAIPNMVVIAPTDYYHTKNVIRTIAEYKGPVYVRMPRRDTEIIYENEEEATFEIGK</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>GFIQLRQGKDITLVASGIMVSRAIEAADYLKELGIEASVIDLFKIKPLPEELKPLLIDQS</entry><entry>241</entry></row><row><entry /><entry /><entry>G I L  G+D+T++A+G  V  A+ A + LKE GI A ++++  IKP+ EE+     D</entry></row><row><entry>Sbjct:</entry><entry>189</entry><entry>GKI-LVDGEDLTIIATGEEVPEALRAGEILKENGISAEIVEMATIKPIDEEIIKKSKD-F</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>IVTIENHNRIGGIGSALCEWL-SMEKDTTVSRMGIDERFGQVGQMEYLLEEYGLAVKDIVQ</entry><entry>301</entry></row><row><entry /><entry /><entry>+VT+E+H+ IGG+G A+ E + S   +  + R+GI++ FG+ G+ + LL+ YGL  + I +</entry></row><row><entry>Sbjct:</entry><entry>247</entry><entry>VVTVEDHSIIGGLGGAVAEVIASNGLNKKLLRIGINDVFGRSGKADELLKYYGLDGESIAK</entry><entry>307</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 520.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 157

A DNA sequence (GBSx0163) was identified in <i>S. agalactiae </i>&lt;SEQ ID 523&gt; which encodes the amino acid sequence &lt;SEQ ID 524&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00538" num="00538"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2517 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 158

A DNA sequence (GBSx0164) was identified in <i>S. agalactiae </i>&lt;SEQ ID 525&gt; which encodes the amino acid sequence &lt;SEQ ID 526&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00539" num="00539"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="28pt" align="left" /><colspec colname="6" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −6.42</entry><entry>Transmembrane</entry><entry>119-135 (114-145)</entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.10</entry><entry>Transmembrane</entry><entry>33-49 (32-50)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>94-110 (94-111)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.66</entry><entry>Transmembrane</entry><entry>67-83 (60-83)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.3569 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8503&gt; and protein &lt;SEQ ID 8504&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00540" num="00540"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 4</entry><entry /></row><row><entry>SRCFLG: 0</entry></row><row><entry>McG: Length of UR: 22</entry></row><row><entry>   Peak Value of UR: 2.96</entry></row><row><entry>   Net Charge of CR: 2</entry></row><row><entry>McG: Discrim Score: 10.55</entry></row><row><entry>GvH: Signal Score (−7.5): −4.31</entry></row><row><entry>   Possible site: 22</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry>Amino Acid Composition: calculated from 1</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="49pt" align="left" /><colspec colname="4" colwidth="231pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 6</entry><entry>value: −6.42</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><colspec colname="6" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −6.42</entry><entry>Transmembrane</entry><entry>154-170 (149-180)</entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.10</entry><entry>Transmembrane</entry><entry>68-84 (67-85)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.04</entry><entry>Transmembrane</entry><entry>6-22 (2-24)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>129-145 (129-146)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.66</entry><entry>Transmembrane</entry><entry>102-118 (95-118) </entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.56</entry><entry>Transmembrane</entry><entry>29-45 (29-46)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 0.79</entry><entry>285</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 1.78</entry><entry /></row><row><entry>icm1 HYPID: 7 CFP: 0.357</entry></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.3569 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00014" num="00014"><img id="EMI-C00014" he="115.40mm" wi="118.62mm" file="US07939087-20110510-C00014.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00014" attachment-type="cdx" file="US07939087-20110510-C00014.CDX" /><attachment idref="CHEM-US-00014" attachment-type="mol" file="US07939087-20110510-C00014.MOL" /></attachments></chemistry>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 159

A DNA sequence (GBSx0165) was identified in <i>S. agalactiae </i>&lt;SEQ ID 527&gt; which encodes the amino acid sequence &lt;SEQ ID 528&gt;. This protein is predicted to be 30S ribosomal protein S15 (rpsO). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00541" num="00541"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4074(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00542" num="00542"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB13541 GB: Z99112 ribosomal protein S15 (BS18) [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 55/89 (61%), Positives = 71/89 (78%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNDHIKQHKKDHATYRGLMKKI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAI++E+KN++I ++  HE DTGS EVQ+A+LT  IN+LN+H++ HKKDH + RGL+K +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAITQERKNQLINEFKTHESDTGSPEVQIAILTDSINNLNEHLRTHKKDHHSRRGLLKMV</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GHRRNLLAYLRRTDVNRYRELIQSLGLRR</entry><entry>89</entry></row><row><entry /><entry /><entry>G RRNLL YLR  DV RYRELI  LGLRR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GKRRNLLTYLRNKDVTRYRELINKLGLRR</entry><entry>89</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 529&gt; which encodes the amino acid sequence &lt;SEQ ID 530&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00543" num="00543"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3746(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00544" num="00544"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 88/89 (98%), Positives = 88/89 (98%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNDHIKQHKKDHATYRGLMKKI</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLN HIKQHKKDHATYRGLMKKI</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNSHIKQHKKDHATYRGLMKKI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>GHRRNLLAYLRRTDVNRYRELIQSLGLRR</entry><entry>89</entry></row><row><entry /><entry /><entry>GHRRNLLAYLRRTDVNRYRELIQSLGLRR</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GHRRNLLAYLRRTDVNRYRELIQSLGLRR</entry><entry>89</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 160

A DNA sequence (GBSx0166) was identified in <i>S. agalactiae </i>&lt;SEQ ID 531&gt; which encodes the amino acid sequence &lt;SEQ ID 532&gt;. This protein is predicted to be polyribonucleotide nucleotidyltransferase (pnp). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00545" num="00545"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.64</entry><entry>Transmembrane</entry><entry>448-464 (448-464)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1256(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9501&gt; which encodes amino acid sequence &lt;SEQ ID 9502&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00546" num="00546"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAC43595 GB: U29668 polynucleotide phosphorylase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 428/694 (61%), Positives = 532/694 (75%), Gaps = 4/694 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>KQVFEMIFAGKKLVVETGQVAKQANGSVVVRYGDSTVLTAAVMSKKMSTGDFFPLQVNYE</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>K VF + +AG+ L VETGQ+AKQANG+V++RYGD+ VL+ A  SK+    DFFPL VNYE</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>KHVFTIDWAGRTLTVETGQLAKQANGAVMIRYGDTAVLSTATASKEPKPLDFFPLTVNYE</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>EKMYAAGKFPGGFNKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSFDENA</entry><entry>126</entry></row><row><entry /><entry /><entry>E++YA GK PGGF KREGRPS  A L +RLIDRPIRP+FA+GFRNEVQVI+ V+S D+N</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>ERLYAVGKIPGGFIKREGRPSEKAVLASRLIDRPIRPLFADGFRNEVQVISIVMSVDQNC</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>SAPMAAMFGSSLALSISDIPFNGPIAGVQVAYVDGNFIINPTAQEQEASALELTVAGTKE</entry><entry>186</entry></row><row><entry /><entry /><entry>S+ MAAMFGSSLALS+SDIPF GPIAGV V  +D  FIINPT  + E S + L VAGTK+</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>SSEMAAMFGSSLALSVSDIPFEGPIAGVTVGRIDDQFIINPTVDQLEKSDINLVVAGTKD</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>AINMVESGAKELSEEIMLEALLKGHEAVCELIAFQEEIVTAIGKEKAEVELLQVDPELQA</entry><entry>246</entry></row><row><entry /><entry /><entry>AINMVE+GA E+ EEIMLEA++ GHE +  LIAFQEEIV A+GKEK+E++L ++D EL</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>AINMVEAGADEVPEEIMLEAIMFGHEEIKRLIAFQEEIVAAVGKEKSEIKLFEIDEELNE</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>247</entry><entry>EIIATHNIALQAAVQVEEKKAREAATEAVKEVVIGEYEARYAEHEEYDRIMRDVAEILEQ</entry><entry>306</entry></row><row><entry /><entry /><entry>++ A     L  A+QV EK ARE A   VK  V+ ++E    EH+E    ++ V +IL +</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>KVKALAEEDLLKAIQVHEKHAREDAINEVKNAVVAKFEDE--EHDE--DTIKQVKQILSK</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>307</entry><entry>MEHAEVRRLITEDKIRPDGRRVDEIRPLDAEIDFLPQVHGSGLFTRGQTQALSVLTLAPM</entry><entry>366</entry></row><row><entry /><entry /><entry>+   EVRRLITE+K+RPDGR VD+IRPL +E+  LP+ HGSGLFTRGQTQALSV TL  +</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>LVKNEVRRLITEEKVRPDGRGVDQIRPLSSEVGLLPRTHGSGLFTRGQTQALSVCTLGAL</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>367</entry><entry>GEAQIIDGLTPEYKKRFMHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPRLE</entry><entry>426</entry></row><row><entry /><entry /><entry>G+ QI+DGL  E  KRFMHHYNFPQ+SVGETG     GRREIGHGALGERALE V+P  +</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GDVQILDGLGVEESKRFMHHYNFPQFSVGETGPMRGPGRREIGHGALGERALEPVIPSEK</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>427</entry><entry>EFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTVLT</entry><entry>486</entry></row><row><entry /><entry /><entry>+FPY +RLV+EVLESNGS+SQASICA TLA+M  GVPIKAPVAGIAMGL+  G +YTVLT</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>DFPYTVRLVSEVLESNGSTSQASICASTLAMMDAGVPIKAPVAGIAMGLVKSGEHYTVLT</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>487</entry><entry>DIQGLEDHFGDMDFKVAGTREGITALQMDIKIEGITPQILEEALAQAKKARFEILDVLHG</entry><entry>546</entry></row><row><entry /><entry /><entry>DIQG+ED  GDMDFKVAGT +G+TALQMDIKIEG++ +ILEEAL QAKK R EIL+ +</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>DIQGMEDALGDMDFKVAGTEKGVTALQMDIKIEGLSREILEEALQQAKKGRMEILNSMLA</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>547</entry><entry>AIAEPRPQLAPTAPKIDMIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDEEGNVSIFS</entry><entry>606</entry></row><row><entry /><entry /><entry> ++E R +L+  APKI  + I+ DKI+ VIG  G+ I+KII ETGVKIDI+++G + I S</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>TLSESRKELSRYAPKILTMTINPDKIRDVIGPSGKQINKIIEETGVKIDIEQDGTIFISS</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>607</entry><entry>SDQAAIDRTKDIIASLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWTRT</entry><entry>666</entry></row><row><entry /><entry /><entry>+D++   + K II  LVRE +VG++Y  KV RIEKFGAFV +F   D LVHISE+A  R</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>TDESGNQKAKKIIEDLVREVEVGQLYLGKVKRIEKFGAFVEIFSGKDGLVHISELALERV</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>667</entry><entry>ANVADVLEIGEEVDVKVIKIDDKGRVDASMKALL</entry><entry>700</entry></row><row><entry /><entry /><entry>  V DV++IG+E+ VKV +ID +GRV+ S KA+L</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>GKVEDVVKIGDEILVKVTEIDKQGRVNLSRKAVL</entry><entry>694</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 533&gt; which encodes the amino acid sequence &lt;SEQ ID 534&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00547" num="00547"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 28</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.64</entry><entry>Transmembrane</entry><entry>444-460 (444-460)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1256(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00548" num="00548"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 631/708 (89%), Positives = 664/708 (93%), Gaps = 2/708 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MSKQVFEMIFAGKKLVVETGQVAKQANGSVVVRYGDSTVLTAAVMSKKMSTGDFFPLQVN</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>MSKQ F   FAGK LVVE GQVAKQANG+ VVRYGDSTVLTAAVMSKKM+TGDFFPLQVN</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSKQTFTTTFAGKPLVVEVGQVAKQANGATVVRYGDSTVLTAAVMSKKMATGDFFPLQVN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>YEEKMYAAGKFPGGFNKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSFDE</entry><entry>124</entry></row><row><entry /><entry /><entry>YEEKNYAAGKFPGGF KREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLS+DE</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YEEKMYAAGKFPGGFMKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSYDE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>NASAPMAAMFGSSLALSISDIPFNGPIAGVQVAYVDGNFIINPTAQEQEASALELTVAGT</entry><entry>184</entry></row><row><entry /><entry /><entry>NASAPMAAMFGSSLALSISDIPFNGPIAGVQV Y+DG FIINP  ++ EAS LELTVAG+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NASAPMAAMFGSSLALSISDIPFNGPIAGVQVGYIDGEFIINPDKEQMEASLLELTVAGS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>KEAINMVESGAKELSEEIMLEALLKGHEAVCELIAFQEEIVTAIGKEKAEVELLQVDPEL</entry><entry>244</entry></row><row><entry /><entry /><entry>KEAINMVESGAKELSE+IMLEALLKGH+A+ ELIAFQE+IV  +GKEKAEVELLQVD +L</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>KEAINMVESGAKELSEDIMLEALLKGHQAIQELIAFQEQIVAVVGKEKAEVELLQVDVDL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>QAEIIATHNIALQAAVQVEEKKAREAATEAVKEVVIGEYEARYAEHEEYDRIMRDVAEIL</entry><entry>304</entry></row><row><entry /><entry /><entry>QA+I+A +N  LQ AVQVEEKKAREAATEAVKE+V  EYE RYAE E    IMRDVAEIL</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>QADIVAKYNAQLQKAVQVEEKKAREAATEAVKEMVKAEYEERYAEDENLATIMRDVAEIL</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>EQMEHAEVRRLITEDKIRPDGRRVDEIRPLDAEIDFLPQVHGSGLFTRGQTQALSVLTLA</entry><entry>364</entry></row><row><entry /><entry /><entry>EQMEHAEVRRLITEDKIRPDGR++DEIRPLDA +DFLP+VHGSGLFTRGQTQALSVLTLA</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>EQMEHAEVRRLITEDKIRPDGRKIDEIRPLDAVVDFLPKVHGSGLFTRGQTQALSVLTLA</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>PMGEAQIIDGLTPEYKKRFMHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPR</entry><entry>424</entry></row><row><entry /><entry /><entry>PMGE QIIDGL PEYKKRF+HHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLP</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>PMGETQIIDGLAPEYKKRFLHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPS</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>425</entry><entry>LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV</entry><entry>484</entry></row><row><entry /><entry /><entry>LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>485</entry><entry>LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKIEGITPQILEEALAQAKKARFEILDVL</entry><entry>544</entry></row><row><entry /><entry /><entry>LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKI GITPQILEEALAQAKKARFEILDV+</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKIAGITPQILEEALAQAKKARFEILDVI</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>545</entry><entry>HGAIAEPRPQLAPTAPKIDMIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDEEGNVSI</entry><entry>604</entry></row><row><entry /><entry /><entry>   IAEPRP+LAPTAPKID IKIDVDKIKVVIGKGGETIDKIIAETGVKIDID+EGNVSI</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>EATIAEPRPELAPTAPKIDTIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDDEGNVSI</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>605</entry><entry>FSSDQAAIDRTKDIIASLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT</entry><entry>664</entry></row><row><entry /><entry /><entry>+SSDQAAIDRTK+IIA LVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>YSSDQAAIDRTKEIIAGLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>665</entry><entry>RTANVADVLEIGEEVDVKVIKIDDKGRVDASMKALLPRPPKADNPKKE</entry><entry>712</entry></row><row><entry /><entry /><entry>RT NV+DVLE+GE+VDVKVIKID+KGRVDASMKAL+PRPPK +  KKE</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>RTTNVSDVLEVGEDVDVKVIKIDEKGRVDASMKALIPRPPKPE--KKE</entry><entry>706</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 161

A DNA sequence (GBSx0167) was identified in <i>S. agalactiae </i>&lt;SEQ ID 535&gt; which encodes the amino acid sequence &lt;SEQ ID 536&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00549" num="00549"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1293 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 537&gt; which encodes the amino acid sequence &lt;SEQ ID 538&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00550" num="00550"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="84pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.43</entry><entry>Transmembrane</entry><entry>83-99 (83-99)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1171 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00551" num="00551"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 172/248 (69%), Positives = 211/248 (84%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTSTNELDIRLRAFINAPDNFLDSIGLVNALHHSTVWASKEPYAIQVDGQEVVPVFTDIT</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MT +NELDIRLRAFINAPDNFLDS+ LVNA H+  VWA+KEPY I+V+G +V PVFTD</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTKSNELDIRLRAFINAPDNFLDSLALVNAFHNFPVWAAKEPYVIEVEGVKVTPVFTDKE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>DLNHFKEEQESARDMFWESRRSLDVLDEAISHGLAGLVYNLKKEGDFGNSTIFYCEDMVQ</entry><entry>120</entry></row><row><entry /><entry /><entry>D+  FKEEQ+SA+  +W  R +L VL+E I+ G AGL++NLKK+GDFGNSTIF   DM+Q</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DMARFKEEQKSAQSQYWLERSALAVLEEVITSGAAGLIFNLKKKGDFGNSTIFKSSDMIQ</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>FMNNYTTILNQLLNEDNIVADIMDKTYLVPAFVHPREEGSFDRLFPTMSTPEGKSYVPVF</entry><entry>180</entry></row><row><entry /><entry /><entry>FMN+YTT+LN L+++DN+ AD M+K YLVPAFV+P++   +DRLFPTMSTPEGKSYVP F</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>FMNHYTTVLNTLMSDDNVAADTMEKVYLVPAFVYPKDNNHYDRLFPTMSTPEGKSYVPAF</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>SNLLSFEKWYNHNDFGGAFRKAQGVILAWTIDDIYKPRNGENEIDDTFGVAINPFDEQQV</entry><entry>240</entry></row><row><entry /><entry /><entry>SNL SF KWYN +DFGG FRKA+GVIL WTIDDIY+PRNGENE+D+TFGVAINPFD+QQ+</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SNLQSFAKWYNQDDFGGLFRKAEGVILTWTIDDIYQPRNGENELDETFGVAINPFDDQQI</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>LVDWSDVE</entry><entry>248</entry></row><row><entry /><entry /><entry>LVDWS+++</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LVDWSELD</entry><entry>248</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 162

A DNA sequence (GBSx0168) was identified in <i>S. agalactiae </i>&lt;SEQ ID 539&gt; which encodes the amino acid sequence &lt;SEQ ID 540&gt;. This protein is predicted to be serine acetyltransferase (cysE). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00552" num="00552"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="84pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.02</entry><entry>Transmembrane</entry><entry>150-166 (147-168)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1808 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9503&gt; which encodes amino acid sequence &lt;SEQ ID 9504&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00553" num="00553"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB71304 GB: AJ130879 serine acetyltransferase [<i>Clostridium</i></entry><entry /></row><row><entry><i>sticklandii</i>]</entry></row><row><entry>Identities = 92/169 (54%), Positives = 125/169 (73%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>9</entry><entry>KESIAIVKEQDPAARSSLEVILTYPGIKALAAHRLSHFLWNHNFKLLARMHSQFWRFWTQ</entry><entry>68</entry><entry /></row><row><entry /><entry /><entry>KE+I + +E+DPAA+ ++ +++  PGI A+  HR++H L+N     +AR+ SQ  RF T</entry></row><row><entry>Sbjct:</entry><entry>20</entry><entry>KETIEVAREKDPAAKGAINILVNTPGIHAIMFHRVAHSLYNRKHFFIARLISQISRFLTG</entry><entry>79</entry></row><row><entry /></row><row><entry>Query:</entry><entry>69</entry><entry>IEIHPGATISEGVFIDHGSGLVIGETAIVEKGAMLYHGVTLGGTGKDKGKRHPTIRKGAL</entry><entry>128</entry></row><row><entry /><entry /><entry>IEIHPGA I    FIDHG G+VIGETA +    ML+H VTLGGTGKDKGKRHPT+    +</entry></row><row><entry>Sbjct:</entry><entry>80</entry><entry>IEIHPGAQIGRRFFIDHGMGVVIGETAEIGDDVMLFHQVTLGGTGKDKGKRHPTVENNVI</entry><entry>139</entry></row><row><entry /></row><row><entry>Query:</entry><entry>129</entry><entry>ISAHSQIIGPIEVGENAKVGAAAVVLADVPADVTVVGVPAKVVRVHGQK</entry><entry>177</entry></row><row><entry /><entry /><entry>ISA  +++GPI +GEN+K+GA AVVL D+P + T VG+PAKVVR++G+K</entry></row><row><entry>Sbjct:</entry><entry>140</entry><entry>ISAGVKVLGPIVIGENSKIGANAVVLHDIPKNATAVGIPAKVVRLNGEK</entry><entry>188</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 541&gt; which encodes the amino acid sequence &lt;SEQ ID 542&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00554" num="00554"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0141 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00555" num="00555"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 162/193 (83%), Positives = 178/193 (91%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>MGWWKESIAIVKEQDPAARSSLEVILTYPGIKALAAHRLSHFLWNHNFKLLARMHSQFWR</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>MGWWKESIAIVK  DPAAR+SLEVILTYPGIKALAAHRLSHFLW H+FKLLARMHSQFWR</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MGWWKESIAIVKALDPAARNSLEVILTYPGIKALAAHRLSHFLWRHHFKLLARMHSQFWR</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>FWTQIEIHPGATISEGVFIDHGSGLVIGETAIVEKGAMLYHGVTLGGTGKDKGKRHPTIR</entry><entry>124</entry></row><row><entry /><entry /><entry>FWTQIEIHPGA I+ GVFIDHG+GLVIGETAIVEKG MLYHGVTLGGTGKD GKRHPT+R</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FWTQIEIHPGAQIAPGVFIDHGAGLVIGETAIVEKGVMLYHGVTLGGTGKDCGKRHPTVR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>KGALISAHSQIIGPIEVGENAKVGAAAVVLADVPADVTVVGVPAKVVRVHGQKDDLQIRS</entry><entry>184</entry></row><row><entry /><entry /><entry>+GALISAH+Q+IGPI++G NAKVGAAAVVL+DVP DVTVVGVPAK+VRVHGQKD+ QI+S</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>QGALISAHAQVIGPIDIGANAKVGAAAVVLSDVPEDVTVVGVPAKIVRVHGQKDNRQIQS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>IEHDREESYYSSK</entry><entry>197</entry></row><row><entry /><entry /><entry>++  RE SY  SK</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LQKQREVSYQLSK</entry><entry>193</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 163

A DNA sequence (GBSx0169) was identified in <i>S. agalactiae </i>&lt;SEQ ID 543&gt; which encodes the amino acid sequence &lt;SEQ ID 544&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00556" num="00556"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="203pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −5.89</entry><entry>Transmembrane</entry><entry>32-48 (29-49)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.3357 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 164

A DNA sequence (GBSx0170) was identified in <i>S. agalactiae </i>&lt;SEQ ID 545&gt; which encodes the amino acid sequence &lt;SEQ ID 546&gt;. This protein is predicted to be cysteinyl-tRNA synthetase (cysS). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00557" num="00557"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2227 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00558" num="00558"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11870 GB: Z99104 cysteinyl-tRNA synthetase [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 246/465 (52%), Positives = 322/465 (68%), Gaps = 23/465 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>IKIYDTMTRSLQDFIPLNEGKVNMYVCGPTVYNYIHIGNARSVVAFDTIRRYFEYCGYQV</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>I +Y+T+TR  + F+PL EGKV MYVCGPTVYNYIHIGNAR  + +DT+R Y EY GY V</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>ITLYNTLTRQKETFVPLEEGKVKMYVCGPTVYNYIHIGNARPAIVYDTVRNYLEYKGYDV</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>NYISNFTDVDDKIIKGAAEAGMDTKSFSDKFISAFMEDVAALGVKPATKNPRVIDYMDEI</entry><entry>121</entry></row><row><entry /><entry /><entry> Y+SNFTDVDDK+IK A E G D  + S++FI A+ EDV ALG + A  +PRV++ MD I</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>QYVSNFTDVDDKLIKAANELGEDVPTISERFIKAYFEDVGALGCRKADLHPRVMENMDAI</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>IDFVKVLVDKEFAYEANGDVYFRVSKSHHYAKLANKTLEDLEIGASGRVDGEGEIKENPL</entry><entry>181</entry></row><row><entry /><entry /><entry>I+FV  LV K +AYE+ GDVYF+      Y KL+ +++++L  GA  RV   GE KE+ L</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>IEFVDQLVKKGYAYESEGDVYFKTRAFEGYGKLSQQSIDELRSGARIRV---GEKKEDAL</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>DFALWKSAKSGEVSWESPWGKGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNEI</entry><entry>241</entry></row><row><entry /><entry /><entry>DFALWK+AK GE+SW+SPWGKGRPGWHIECS M  + LGD IDIH GG DL FPHH NEI</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>DFALWKAAKEGEISWDSPWGKGRPGWHIECSAMVKKYLGDQIDIHAGGQDLTFPHHENEI</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>AQSEAKTGKTFANYWMHNGFVNVDNEKMSKSLGNFITVHDMLKSVDGQVIRFFLATQQYR</entry><entry>301</entry></row><row><entry /><entry /><entry>AQSEA TGKTFA YW+HNG++N+DNEKMSKSLGNF+ VHD++K  D Q++RFF+ +  YR</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>AQSEALTGKTFAKYWLHNGYINIDNEKMSKSLGNFVLVHDIIKQHDPQLLRFFMLSVHYR</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>KPVNFTEKAVHDAEVNLKYLKNTF-----------NLPIQENANDEELEQFVKAFQGAMD</entry><entry>350</entry></row><row><entry /><entry /><entry> P+N++E+ + + +     LK  +           NL   ++   E++E+  KAF+  MD</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>HPINYSEELLENTKSAFSRLKTAYSNLQHRLNSSTNLTEDDDQWLEKVEEHRKAFEEEMD</entry><entry>359</entry></row><row><entry /></row><row><entry>Query:</entry><entry>351</entry><entry>DDFNTANGITVIFEMAKWIN--------SGHYTSRVKETFAELLEIFGI-VFQEEVLDAD</entry><entry>401</entry></row><row><entry /><entry /><entry>DDFNTAN I+V+F++AK  N        + H  +   E F  ++ + G  + ++E+LD +</entry></row><row><entry>Sbjct:</entry><entry>360</entry><entry>DDFNTANAISVLFDLAKHANYYLQKDHTADHVITAFIEMFDRIVSVLGFSLGEQELLDQE</entry><entry>419</entry></row><row><entry /></row><row><entry>Query:</entry><entry>402</entry><entry>IESLIEQRQEARANRDFATADRIRDELAKQGIKLLDTKDGVRWTR</entry><entry>446</entry></row><row><entry /><entry /><entry>IE LIE+R EAR NRDFA +D+IRD+L    I L DT  G RW R</entry></row><row><entry>Sbjct:</entry><entry>420</entry><entry>IEDLIEKRNEARRNRDFALSDQIRDQLKSMNIILEDTAQGTRWKR</entry><entry>464</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 547&gt; which encodes the amino acid sequence &lt;SEQ ID 548&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00559" num="00559"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1765(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00560" num="00560"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 357/447 (79%), Positives = 401/447 (88%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MIKIYDTMTRSLQDFIPLNEGKVNMYVCGPTVYNYIHIGNARSVVAFDTIRRYFEYCGYQ</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MIKIYDTMTRSL+ F+PL E  VN+YVCGPTVYNYIHIGNARS VAFDTIRRYFEY GYQ</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MIKIYDTMTRSLRKFVPLTENTVNIYVCGPTVYNYIHIGNARSAVAFDTIRRYFEYTGYQ</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>VNYISNFTDVDDKIIKGAAEAGMDTKSFSDKFISAFMEDVAALGVKPATKNPRVIDYMDE</entry><entry>120</entry></row><row><entry /><entry /><entry>VNYISNFTDVDDKIIK A +AG+  K  SD+FI+AF+ED  ALGVKPAT+NPRV+DY+ E</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>VNYISNFTDVDDKIIKAATQAGVSPKELSDRFIAAFIEDTKALGVKPATQNPRVMDYIAE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>IIDFVKVLVDKEFAYEANGDVYFRVSKSHHYAKLANKTLEDLEIGASGRVDGEGEIKENP</entry><entry>180</entry></row><row><entry /><entry /><entry>II FV+ L++K+FAYEA+GDVYFRV KS HYAKLANKTL +LE+GASGR D E  +KENP</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IISFVESLIEKDFAYEADGDVYFRVEKSEHYAKLANKTLSELEVGASGRTDAETALKENP</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LDFALWKSAKSGEVSWESPWGKGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE</entry><entry>240</entry></row><row><entry /><entry /><entry>LDFALWKSAK+GEVSW+SPWG GRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LDFALWKSAKAGEVSWDSPWGFGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>IAQSEAKTGKTFANYWMHNGFVNVDNEKMSKSLGNFITVHDMLKSVDGQVIRFFLATQQY</entry><entry>300</entry></row><row><entry /><entry /><entry>IAQSEAKTGKTFANYWMHNGFV VDNEKMSKSLGNF+TVHDML++VDGQV+RFFLATQQY</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>IAQSEAKTGKTFANYWMHNGFVTVDNEKMSKSLGNFVTVHDMLQTVDGQVLRFFLATQQY</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>RKPVNFTEKAVHDAEVNLKYLKNTFNLPIQENANDEELEQFVKAFQGAMDDDFNTANGIT</entry><entry>360</entry></row><row><entry /><entry /><entry>RKP+NFTEK +HDAE+NLKYLKNT   P+ E A+++EL+QFV AFQ AMDDDFNTANGIT</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>RKPINFTEKTIHDAEINLKYLKNTLQQPLTETADEQELKQFVIAFQDAMDDDFNTANGIT</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>361</entry><entry>VIFEMAKWINSGHYTSRVKETFAELLEIFGIVFQEEVLDADIESLIEQRQEARANRDFAT</entry><entry>420</entry></row><row><entry /><entry /><entry>V+F+MAKWINSG YT  VK  F ++L +FGI+F+EEVL+ DIE+LI +RQEARANRDFAT</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>VVFDMAKWINSGSYTEPVKSAFEKMLAVFGIIFEEEVLEVDIEALIAKRQEARANRDFAT</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>421</entry><entry>ADRIRDELAKQGIKLLDTKDGVRWTRD</entry><entry>447</entry></row><row><entry /><entry /><entry>AD IRD+LA QGIKLLDTKDGVRW RD</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>ADAIRDQLAVQGIKLLDTKDGVRWLRD</entry><entry>447</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 165

A DNA sequence (GBSx0171) was identified in <i>S. agalactiae </i>&lt;SEQ ID 549&gt; which encodes the amino acid sequence &lt;SEQ ID 550&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00561" num="00561"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0259(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9505&gt; which encodes amino acid sequence &lt;SEQ ID 9506&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00562" num="00562"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11871 GB: Z99104 similar to hypothetical proteins</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 58/122 (47%), Positives = 87/122 (70%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>DVRLINGIALAFEGDAVYSLYIRRHLIMQGFTKPNQLHRKATQYVSANAQALLINAMLEE</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>D + +NG+ALA+ GDA++ +Y+R HL+ QGFTKPN LH+K+++ VSA +QA ++  +  +</entry></row><row><entry>Sbjct:</entry><entry>9</entry><entry>DSKQLNGLALAYIGDAIFEVYVRHHLLKQGFTKPNDLHKKSSRIVSAKSQAEILFFLQNQ</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>NILTDEEQLIYKRGRNANSHTKAKNADIITYRMSTGFEALMGYLDMTGQIKRLETLIQWC</entry><entry>122</entry></row><row><entry /><entry /><entry>+  T+EE+ + KRGRNA S T  KN D+ TYR ST FEAL+GYL +  + +RL  L+</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>SFFTEEEEAVLKRGRNAKSGTTPKNTDVQTYRYSTAFEALLGYLFLEKKEERLSQLVAEA</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>IE</entry><entry>124</entry></row><row><entry /><entry /><entry>I+</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>IQ</entry><entry>130</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 551&gt; which encodes the amino acid sequence &lt;SEQ ID 552&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00563" num="00563"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00564" num="00564"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 99/127 (77%), Positives = 111/127 (86%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>IDVRLINGIALAFEGDAVYSLYIRRHLIMQGFTKPNQLHRKATQYVSANAQALLINAMLE</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+DV LINGIALAFEGDAVYS Y+RRHLI QG TKP+QLHR AT+YVSA AQA LI AMLE</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>VDVNLINGIALAFEGDAVYSYYVRRHLIFQGKTKPSQLHRLATRYVSAKAQANLIQAMLE</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>ENILTDEEQLIYKRGRNANSHTKAKNADIITYRMSTGFEALMGYLDMTGQIKRLETLIQW</entry><entry>121</entry></row><row><entry /><entry /><entry>  +LT++E+ IYKRGRN NSHTKAKNADIITYRMSTGFEA+MGYLDM GQ +RLE LI+W</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>AQLLTEKEEDIYKRGRNTNSHTKAKNADIITYRMSTGFEAIMGYLDMMGQKERLEELIRW</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>CIETIEK</entry><entry>128</entry></row><row><entry /><entry /><entry>CIE +EK</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>CIEYVEK</entry><entry>131</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 166

A DNA sequence (GBSx0172) was identified in <i>S. agalactiae </i>&lt;SEQ ID 553&gt; which encodes the amino acid sequence &lt;SEQ ID 554&gt;. This protein is predicted to be spoU rRNA methylase family protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00565" num="00565"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1478 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00566" num="00566"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11872 GB: Z99104 similar to hypothetical proteins [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 113/244 (46%), Positives = 163/244 (66%), Gaps = 6/244 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="14pt" align="center" /><colspec colname="6" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>ESSDLVYGLHAVTESLRANTG-NKLYLQDDLRGKNVDKVKALATEKKVSISWTPKKTLSD</entry><entry>69</entry><entry /><entry /></row><row><entry /><entry /><entry>+  D V G +AV E+L+++    KL++ ++       +V  LA ++ ++I + P+K L</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>QQHDYVIGKNAVIETLKSDRKLYKLWMAENTVKGQAQQVIELAKKQGITIQYVPRKKLDQ</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>70</entry><entry>MTNGGVHQGFVLKVSEFAYADLSEIMTKAENE-ENPLILILDGLTDPHNLGSILRTADAT</entry><entry>128</entry></row><row><entry /><entry /><entry>M  G  HQG V +V+ + YA+L ++   AE + E P  LILD L DPHNLGSI+RTADA</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>MVTGQ-HQGVVAQVAAYEYAELDDLYKAAEEKNEQPFFLILDELEDPHNLGSIMRTADAV</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>129</entry><entry>NVTGIIIPKHRSVGVTPVVSKTSTGAVEHVPIARVTNLSQTLDTLKDKEFWIFGTDMNGT</entry><entry>188</entry></row><row><entry /><entry /><entry>   GI+IPK R+VG+T  V+K STGA+EH+P+ARVTNL++TL+ +K++  W+ GTD +</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>GAHGIVIPKRRAVGLTTTVAKASTGAIEHIPVARVTNLARTLEEMKERGIWVVGTDASAR</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>189</entry><entry>PSHKWNTKGK--LALVIGNEGKGISHNIKKQVDEMITIPMNGHVQSLNASVAAAILMYEV</entry><entry>246</entry></row><row><entry /><entry /><entry>   + N  G   LALVIG+EGKG+   +K++ D +I +PM G V SLNASVAA +LMYEV</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>EDFR-NMDGNMPLALVIGSEGKGMGRLVKEKCDFLIKLPMAGKVTSLNASVAAGLLMYEV</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>247</entry><entry>FRNR</entry><entry>250</entry></row><row><entry /><entry /><entry>+R R</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YRKR</entry><entry>244</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 555&gt; which encodes the amino acid sequence &lt;SEQ ID 556&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00567" num="00567"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1037 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00568" num="00568"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 206/248 (83%), Positives = 225/248 (90%), Gaps = 1/248 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>MKDKQFKEESSDLVYGLHAVTESLRANTGNKLYLQDDLRGKNVDKVKALATEKKVSISWT</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>M+DK    E++D+VYG+HAVTESL+ANTGNKLY+Q+DLRGK VD +K+LAT+KKV+ISWT</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>MEDKD-TIETNDIVYGVHAVTESLQANTGNKLYIQEDLRGKKVDNIKSLATQKKVAISWT</entry><entry>68</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>PKKTLSDMTNGGVHQGFVLKVSEFAYADLSEIMTKAENEENPLILILDGLTDPHNLGSIL</entry><entry>122</entry></row><row><entry /><entry /><entry>PKKTLS MT+G VHQGFVL+VS FAY D+ EI+  AE E NPLILILDGLTDPHNLGSIL</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>PKKTLSQMTDGAVHQGFVLRVSAFAYTDVDEILEIAEQEANPLILILDGLTDPHNLGSIL</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>RTADATNVTGIIIPKHRSVGVTPVVSKTSTGAVEHVPIARVTNLSQTLDTLKDKEFWIFG</entry><entry>182</entry></row><row><entry /><entry /><entry>RTADATNV G+IIPKHRSVGVTPVVSKTSTGAVEH+PIARVTNLSQTLD LK + FWIFG</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>RTADATNVCGVIIPKHRSVGVTPVVSKTSTGAVEHIPIARVTNLSQTLDKLKARGFWIFG</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>TDMNGTPSHKWNTKGKLALVIGNEGKGISHNIKKQVDEMITIPMNGHVQSLNASVAAAIL</entry><entry>242</entry></row><row><entry /><entry /><entry>TDMNGTPS  WNT GKLALVIGNEGKGIS NIKKQVDEMITIPMNGHVQSLNASVAAAIL</entry></row><row><entry>Sbjct:</entry><entry>189</entry><entry>TDMNGTPSDCWNTNGKLALVIGNEGKGISTNIKKQVDEMITIPMNGHVQSLNASVAAAIL</entry><entry>248</entry></row><row><entry /></row><row><entry>Query:</entry><entry>243</entry><entry>MYEVFRNR</entry><entry>250</entry></row><row><entry /><entry /><entry>MYEVFRNR</entry></row><row><entry>Sbjct:</entry><entry>249</entry><entry>MYEVFRNR</entry><entry>256</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 167

A DNA sequence (GBSx0173) was identified in <i>S. agalactiae </i>&lt;SEQ ID 557&gt; which encodes the amino acid sequence &lt;SEQ ID 558&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00569" num="00569"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2187 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00570" num="00570"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11873 GB: Z99104 similar to hypothetical proteins </entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 67/147 (45%), Positives = 94/147 (63%), Gaps = 2/147 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>ILLVDGYNMIAFWKDTRQLFKSNRLEEAREVLLRKLNHYAHFEHIDIICVFDAQYVPGVR</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>ILLVDGYNMI  W   + L K+N  EEAR+VL++K+  Y  +    +I VFDA  V G+</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>ILLVDGYNMIGAWPQLKDL-KANSFEEARDVLIQKMAEYQSYTGNRVIVVFDAHLVKGLE</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>QRYDQYKISVIFTEEDETADSYIERAAAELNQSVLNLVSVATSDLNEQWTIFSQGALRVS</entry><entry>125</entry></row><row><entry /><entry /><entry>++   +++ VIFT+E+ETAD  IE+ A  LN ++   + VATSD  EQW IF QGALR S</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>KKQTNHRVEVIFTKENETADERIEKLAQALN-NIATQIHVATSDYTEQWAIFGQGALRKS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>ARELEQRVATVKSDLDKMSSQIDLSTP</entry><entry>152</entry></row><row><entry /><entry /><entry>AREL + V T++  +++   +I    P</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>ARELLREVETIERRIERRVRKITSEKP</entry><entry>147</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 559&gt; which encodes the amino acid sequence &lt;SEQ ID 560&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00571" num="00571"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2465(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00572" num="00572"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 130/167 (77%), Positives = 149/167 (88%), Gaps = 1/167 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KHSILLVDGYNMIAEWKDTRQLFKSNRLEEAREVLLRKLNHYAHFEHIDIICVFDAQYVP</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>K  ILLVDGYNMIAFW+ TRQLFK+N+L++AR  LL KLNHYAHFE+I+IICVFDAQYVP</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KKRILLVDGYNMIAFWQSTRQLFKTNQLDQARNTLLTKLNHYAHFENINIICVFDAQYVP</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>GVRQRYDQYKISVIFTEEDETADSYIERAAAELNQSVLNLVSVATSDLNEQWTIFSQGAL</entry><entry>122</entry></row><row><entry /><entry /><entry>G+RQRYDQY ISV+FTEEDETADSYIER AAELN + +++V VATSDLNEQWTIFSQGAL</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>GLRQRYDQYYISVVFTEEDETADSYIERMAAELN-TAIHMVEVATSDLNEQWTIFSQGAL</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>RVSARELEQRVATVKSDLDKMSSQIDLSTPKLRPWNDEQLGKLKDFL</entry><entry>169</entry></row><row><entry /><entry /><entry>RV+ARELEQRV TVK+DLDKMS  IDL TPKLRP++  QL +LKDF+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>RVTARELEQRVHTVKADLDKMSRDIDLKTPKLRPFDQGQLIQLKDFM</entry><entry>167</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 168

A DNA sequence (GBSx0174) was identified in <i>S. agalactiae </i>&lt;SEQ ID 561&gt; which encodes the amino acid sequence &lt;SEQ ID 562&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00573" num="00573"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4889(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00574" num="00574"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB12951 GB: Z99109 yits [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 100/284 (35%), Positives = 157/284 (55%), Gaps = 6/284 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTFKILTDSTSDLDEKWAQEHNVDIIGLTIELDGKTYETVGDEKITSDFLLERMQEGAKP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MT  ++ DS +DL   + +E  +  I L +L  K +E      I +D + E MQ G  P</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTVHLIADSATDLPRSYFEEKGIGFIPLRVSLGDKEFEDA--VTIHADQIFEAMQNGETP</entry><entry>58</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TTSQINVGQFEEVFSTYAENDHALLYLALSSHLSGTYQSATIAREMVLDKYPDAQIEIVD</entry><entry>120</entry></row><row><entry /><entry /><entry> TSQ +    + VF  YAE     LY+A SS LSGTYQ+A +    V +++PD  + ++D</entry></row><row><entry>Sbjct:</entry><entry>59</entry><entry>KTSQASPQTIKNVFLQYAETGDPALYIAFSSGLSGTYQTAVMIANEVKEEFPDFDLRVID</entry><entry>118</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TMAASCGEGVLAMLATKERQEGKSLEEVKQKIESLLPKLNTYFLVDDLNHLMRSGRLSKG</entry><entry>180</entry></row><row><entry /><entry /><entry>+  AS G G+    A      G +++E++  +++   +L   F VDDL +L R GR+SK</entry></row><row><entry>Sbjct:</entry><entry>119</entry><entry>SKCASLGYGLAVRHAADLCINGNTIQEIETSVKNFCSQLEHIFTVDDLTYLARGGRISKT</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>AAIIGSVAKIKPLLKLDSEGKLVPFAKTRGRKKGIK---EIVTQATKTLSYSTLIIAYSG</entry><entry>237</entry></row><row><entry /><entry /><entry>+A +G +  IKPLL+++ +GKLVP  K RG+KK  K   E++ +     S  T+ I+Y+</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>SAFVGGLLNIKPLLQME-DGKLVPLEKIRGQKKLFKRIIELMKERGDDWSNQTVGISYAA</entry><entry>237</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>EKDSAQVMKEQLLADERIEEVIIRPLGPVISAHVGSGALALFSL</entry><entry>281</entry></row><row><entry /><entry /><entry> K+ A  MK  +    + +E+I+ P+   I +H G G LA+F L</entry></row><row><entry>Sbjct:</entry><entry>238</entry><entry>NKEKATDMKHLIEEAFKPKEIIMHPISSAIGSHAGPGTLAIFFL</entry><entry>281</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 563&gt; which encodes the amino acid sequence &lt;SEQ ID 564&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00575" num="00575"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3247(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00576" num="00576"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 167/286 (58%), Positives = 227/286 (78%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTFKILTDSTSDLDEKWAQEHNVDIIGLTIELDGKTYETVGDEKITSDFLLERMQEGAKP</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MTF I+TDST+DL++ WA++H++ +IGLTI  DG+ YETVG  +I+SD+LL++M+ G+ P</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTFTIMTDSTADLNQTWAEDHDIVLIGLTILCDGEVYETVGPNRISSDYLLKKMKAGSHP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>TTSQINVGQFEEVFSTYAENDHALLYLALSSHLSGTYQSATIAREMVLDKYPDAQIEIVD</entry><entry>120</entry></row><row><entry /><entry /><entry> TSQINVG+FE+VF  +A N+ ALLYLA SS LSGTYQSA +AR++V + YPDA IEIVD</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>QTSQINVGEFEKVFREHARNNKALLYLAFSSVLSGTYQSALMARDLVREDYPDAVIEIVD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>TMAASCGEGVLAMLATKERQEGKSLEEVKQKIESLLPKLNTYFLVDDLNHLMRSGRLSKG</entry><entry>180</entry></row><row><entry /><entry /><entry>T+AA+ GEG L +LA + R  GK+L E K  +E+++P+L TYFLVDDL HLMR GRLSKG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TLAAAGGEGYLTILAAEARDSGKNLLETKDIVEAVIPRLRTYFLVDDLFHLMRGGRLSKG</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>AAIIGSVAKIKPLLKLDSEGKLVPFAKTRGRKKGIKEIVTQATKTLSYSTLIIAYSGEKD</entry><entry>240</entry></row><row><entry /><entry /><entry>+A +GS+A IKPLL +D EGKLVP AK RGR+K IKE+V Q  K ++ ST+I++Y+ ++</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SAFLGSLASIKPLLWIDEEGKLVPIAKIRGRQKAIKEMVAQVEKDIADSTVIVSYTSDQG</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>SAQVMKEQLLADERIEEVIIRPLGPVISAHVGSGALALFSLGEENR</entry><entry>286</entry></row><row><entry /><entry /><entry>SA+ ++E+LLA E I +V++ PLGPVISAHVG   LA+F +G+ +R</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>SAEKLREELLAHENISDVLMMPLGPVISAHVGPNTLAVFVIGQNSR</entry><entry>286</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 169

A DNA sequence (GBSx0175) was identified in <i>S. agalactiae </i>&lt;SEQ ID 565&gt; which encodes the amino acid sequence &lt;SEQ ID 566&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00577" num="00577"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.76</entry><entry>Transmembrane</entry><entry>43-59 (40-62)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4503(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 170

A DNA sequence (GBSx0176) was identified in <i>S. agalactiae </i>&lt;SEQ ID 567&gt; which encodes the amino acid sequence &lt;SEQ ID 568&gt;. This protein is predicted to be ribosomal protein L13 (rplM). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00578" num="00578"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3426(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9507&gt; which encodes amino acid sequence &lt;SEQ ID 9508&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00579" num="00579"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB03887 GB: AP001507 ribosomal protein L13 [<i>Bacillus halodurans</i>]</entry><entry /></row><row><entry>Identities = 89/144 (61%), Positives = 113/144 (77%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>36</entry><entry>KTTFMAKPGQVERKWYVVDAADVPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAE</entry><entry>95</entry><entry /></row><row><entry /><entry /><entry>+TT+MAKP +VERKWYVVDA    LGRL++ VAS+LRGK+KPT+TPH DTGD VI+INAE</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>RTTYMAKPNEVERKWYVVDAEGQTLGRLASEVASILRGKHKPTYTPHVDTGDHVIIINAE</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>96</entry><entry>KVKLTGKKASDKIYYTHSMYPGGLKQISAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGM</entry><entry>155</entry></row><row><entry /><entry /><entry>K+ LTG K  DKIYY HS +PGGLK+  A ++R+    +++E ++KGMLP NTLGR QGM</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>KIHLTGNKLQDKIYYRHSGHPGGLKETRAADMRANKPEKMLELAIKGMLPKNTLGRKQGM</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>156</entry><entry>KLKVFVGGEHTHAAQQPEVLDISG</entry><entry>179</entry></row><row><entry /><entry /><entry>KL V+ G EH H AQ+PEV ++ G</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>KLHVYAGSEHKHQAQKPEVYELRG</entry><entry>145</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 569&gt; which encodes the amino acid sequence &lt;SEQ ID 570&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00580" num="00580"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4249(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00581" num="00581"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 167/184 (90%), Positives = 171/184 (92%), Gaps = 4/184 (2%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MFTPFVRPRNLSNTLVDRNIHT--CKQ-KRIRIGEIMNKTTFMAKPGQVERKWYVVDAAD</entry><entry>57</entry><entry /></row><row><entry /><entry /><entry>+FTPF RPRNL NT  D   H   CKQ  RIRIGEIMNKTTFMAKPGQVERKWYVVDAAD</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LFTPFERPRNLPNTF-DGTEHPSPCKQILRIRIGEIMNKTTFMAKPGQVERKWYVVDAAD</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>58</entry><entry>VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKASDKIYYTHSMYPG</entry><entry>117</entry></row><row><entry /><entry /><entry>VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKA+DK+YYTHSMYPG</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKATDKVYYTHSMYPG</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>GLKQISAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI</entry><entry>177</entry></row><row><entry /><entry /><entry>GLK I+AGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>GLKSITAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>SGLI</entry><entry>181</entry></row><row><entry /><entry /><entry>SGLI</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>SGLI</entry><entry>183</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 171

A DNA sequence (GBSx0177) was identified in <i>S. agalactiae </i>&lt;SEQ ID 571&gt; which encodes the amino acid sequence &lt;SEQ ID 572&gt;. This protein is predicted to be 30S ribosomal protein S9 (rpsI). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00582" num="00582"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1761(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00583" num="00583"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB11926 GB: Z99104 ribosomal protein S9 [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 88/130 (67%), Positives = 105/130 (80%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAQAQYAGTGRRKNAVARVRLVPGTGKITINKKDVEEYIPHADLRLVINQPFAVTSTQGS</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAQ QY GTGRRK++VARVRLVPG G+I +N +++ E+IP A L   I QP  +T T G+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YDVFVNVVGGGYAGQSGAIRHGISRALLEVDPDFRDSLKRAGLLTRDARMVERKKPGLKK</entry><entry>120</entry></row><row><entry /><entry /><entry>YDV VNV GGG +GQ+GAIRHGI+RALLE DP++R +LKRAGLLTRDARM ERKK GLK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>ARKASQFSKR</entry><entry>130</entry></row><row><entry /><entry /><entry>AR+A QFSKR</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>ARRAPQFSKR</entry><entry>130</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 573&gt; which encodes the amino acid sequence &lt;SEQ ID 574&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00584" num="00584"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1865(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00585" num="00585"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 124/130 (95%), Positives = 129/130 (98%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MAQAQYAGTGRRKNAVARVRLVPGTGKITINKKDVEEYIPHADLRLVINQPFAVTSTQGS</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MAQAQYAGTGRRKNAVARVRLVPGTGKIT+NKKDVEEYIPHADLRL+INQPFAVTST+GS</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAQAQYAGTGRRKNAVARVRLVPGTGKITVNKKDVEEYIPHADLRLIINQPFAVTSTEGS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YDVFVNVVGGGYAGQSGAIRHGISRALLEVDPDFRDSLKRAGLLTRDARMVERKKPGLKK</entry><entry>120</entry></row><row><entry /><entry /><entry>YDVFVNVVGGGY GQSGAIRHGI+RALL+VDPDFRDSLKRAGLLTRDARMVERKKPGLKK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YDVFVNVVGGGYGGQSGAIRHGIARALLQVDPDFRDSLKRAGLLTRDARMVERKKPGLKK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>ARKASQFSKR</entry><entry>130</entry></row><row><entry /><entry /><entry>ARKASQFSKR</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>ARKASQFSKR</entry><entry>130</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 172

A DNA sequence (GBSx0078) was identified in <i>S. agalactiae </i>&lt;SEQ ID 575&gt; which encodes the amino acid sequence &lt;SEQ ID 576&gt;. This protein is predicted to be recombinase (b1345). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00586" num="00586"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1939(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00587" num="00587"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAG29618 GB: AF217235 integrase-like protein [<i>Staphylococcus</i></entry><entry /></row><row><entry><i>aureus</i>]</entry></row><row><entry>Identities = 127/386 (32%), Positives = 205/386 (52%), Gaps = 18/386 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>IHKYPSKKAKNGYLYFVKIYMVKD---SQRADHIKRGFRTRKEAKDYEARLIYLKASGKL</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>I KY  K     Y++    Y+  D    ++    +RGF+T +EAK  EA+L   +</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>IKKYKKKDGSTAYMFVA--YLGTDPITGKQKRTTRRGFKTEREAKIAEAKL---QTEVSQ</entry><entry>56</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>EEFIKPTHKTYNEIFEKWYQAYQDMVEPTTASRTLDMFRLHILPVMGDLPISKISPLDCQ</entry><entry>119</entry></row><row><entry /><entry /><entry>  F+     T+ E++E W + YQ+ V  +T  R L +F   IL    D+PI KI+   CQ</entry></row><row><entry>Sbjct:</entry><entry>57</entry><entry>NGFLNNDITTFKEVYELWLEQYQNTVRESTYQRVLTLFDTAILEHFQDVPIKKITVPYCQ</entry><entry>116</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>NFITDKAKTFKNIKQIKSYTGKVFDFAIKMKLLKHNPMAEIIMPKRKKTRIE---NYWTV</entry><entry>176</entry></row><row><entry /><entry /><entry>  I    K + +IK I+ YT  VF +A+ +K++  NP A    P++K+ + +    Y++</entry></row><row><entry>Sbjct:</entry><entry>117</entry><entry>KVINKWNKKYSDIKAIRIYTSNVFKYAVSLKIIVDNPFAHTKAPRKKEAQQDASTKYYSS</entry><entry>176</entry></row><row><entry /></row><row><entry>Query:</entry><entry>177</entry><entry>QELQEFLAIVLQEEPYKHYALFRLLAYSGLRKGELYALKWADIDFQTETLSVDKSLGR-L</entry><entry>235</entry></row><row><entry /><entry /><entry> EL++FL  V  E+   +YA+FR LA++G R+GEL AL W DIDF  +T+S++K+  R</entry></row><row><entry>Sbjct:</entry><entry>177</entry><entry>DELKQFLTFV--EDDPLYYAIFRTLAFTGFRRGELMALTWNDIDFTKQTISINKTCARGA</entry><entry>234</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>DGQAIEKGTKNDFSVRKIKLDSETISILQEWKSISQKEKAQLAVAPLSIEQDFLFTYCTR</entry><entry>295</entry></row><row><entry /><entry /><entry>+ + + +  K   S R I +D +T S+L+ W++  + E  +      S +   +FT</entry></row><row><entry>Sbjct:</entry><entry>235</entry><entry>NYKLVIQEPKTKSSHRTISIDDKTASVLKSWRTHQRVESLKYG-HNTSDKHQHVFTTVRD</entry><entry>293</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>SGSIEPLHADYINNVLSRIIRKHGLKKISPHGFRHTHATLMIEIGVDPVNTAKRLGHASS</entry><entry>355</entry></row><row><entry /><entry /><entry>+   +PL+ ++ N  L  I  K+  K+I  HGFRHTH +L+ E G+       RLGH</entry></row><row><entry>Sbjct:</entry><entry>294</entry><entry>N---KPLYPEHCNKALDLICEKNSFKRIKVHGFRHTHCSLLFEAGLSIQEVQDRLGHGDI</entry><entry>350</entry></row><row><entry /></row><row><entry>Query:</entry><entry>356</entry><entry>QMTLDTYSHSTTTGEDRSVKQFADYL</entry><entry>381</entry></row><row><entry /><entry /><entry>+ T+D Y+H T    D+   +FA Y+</entry></row><row><entry>Sbjct:</entry><entry>351</entry><entry>KTTMDIYAHVTEKQRDQVADKFAKYI</entry><entry>376</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 577&gt; which encodes the amino acid sequence &lt;SEQ ID 578&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00588" num="00588"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3445(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00589" num="00589"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 109/386 (28%), Positives = 185/386 (47%), Gaps = 28/386 (7%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>IHKYPSKKAKNGYL-YFVKIYMVKDSQRADHIKRGF--RTRKEA--KDYEARLIYLKASG</entry><entry>57</entry><entry /></row><row><entry /><entry /><entry>I K    K KNG + Y   IY+  D      +K     RTRKE   K   A+  +L</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>IMKITEHKKKNGTIVYRASIYLGIDQMTGKRVKTSITGRTRKEVNQKAKHAQFDFLSNGS</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>58</entry><entry>KLEEFIKPTHKTYNEIFEKWYQAYQDMVEPTTASRTLDMFRLHILPVMGDLPISKISPLD</entry><entry>117</entry></row><row><entry /><entry /><entry> ++   K   KT+ E+   W + Y+  V+P T   T+     HI+P +G++ + KI+  D</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>TIKR--KVVIKTFKELSHLWLETYKLTVKPQTYDATVTRLNRHIMPTLGNMKVDKITASD</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>CQNFITDKAKTFKNIKQIKSYTGKVFDFAIKMKLLKHNPMAEIIMPKRK---KTRIENYW</entry><entry>174</entry></row><row><entry /><entry /><entry> Q  I   +K + N   ++S   KV    + + L+ +N   +II+P+++   K +++ +</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>IQMLINRLSKYYVNYTAVRSVIRKVLQQGVLLGLIDYNSARDIILPRKQPNAKKKVK-FI</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>175</entry><entry>TVQELQEFLAIVLQEEPYKHY------ALFRLLAYSGLRKGELYALKWADIDFQTETLSV</entry><entry>228</entry></row><row><entry /><entry /><entry>   +L+ FL   L+   +K Y       L++LL  +GLR GE  AL+W DID +  T+++</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>DPSDLKSFLE-HLETSQHKRYNLYFDAVLYQLLLSTGLRIGEACALEWGDIDLENGTIAI</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>229</entry><entry>DKSLGRLDGQAIEKGTKNDFSVRKIKLDSETISILQEWKSISQKEKAQLAVAPLSIEQDF</entry><entry>288</entry></row><row><entry /><entry /><entry>+K+  +          K     R I +D +T+  L+    + Q  + QL     +   +</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>NKTYNK--NLKFLSTAKTQSGNRVISVDKKTLRSLK----LYQMRQRQLFNEVGARVSEV</entry><entry>295</entry></row><row><entry /></row><row><entry>Query:</entry><entry>289</entry><entry>LFTYCTRSGSIEPLHADYINNVLSRIIRKHGLKKISPHGFRHTHATLMIEIGVDPVNTAK</entry><entry>348</entry></row><row><entry /><entry /><entry>+F   TR    +  +A    + L    ++ G+++ + H FRHTHA+L++  G+</entry></row><row><entry>Sbjct:</entry><entry>296</entry><entry>VFATPTR----KYFNASVRQSALDTRCKEAGIERFTFHAFRHTHASLLLNAGISYKELQY</entry><entry>351</entry></row><row><entry /></row><row><entry>Query:</entry><entry>349</entry><entry>RLGHASSQMTLDTYSHSTTTGEDRSV</entry><entry>374</entry></row><row><entry /><entry /><entry>RLGHA+  MTLDTY H +   E  +V</entry></row><row><entry>Sbjct:</entry><entry>352</entry><entry>RLGHANISMTLDTYGHLSKGKEKEAV</entry><entry>377</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 173

A DNA sequence (GBSx0179) was identified in <i>S. agalactiae </i>&lt;SEQ ID 579&gt; which encodes the amino acid sequence &lt;SEQ ID 580&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00590" num="00590"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2477(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00591" num="00591"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF63067 GB: AF158600 putative DNA binding protein</entry><entry /></row><row><entry>[<i>Streptococcus thermophilus </i>bacteriophage Sfill]</entry></row><row><entry>Identities = 32/70 (45%), Positives = 46/70 (65%), Gaps = 3/70 (4%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>NRLKELRKDKGLTQADLAKVINTNQSQYGKYENGKTSLSIENSKILADFFGVSIPYLLGL</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>NRL  LR+ + +T+ +LA+ I  ++    K E+G + +S   +K LADFFGVS+ YLLGL</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>NRLYLLRESRKITRVELAEKIGVSKLTVLKLEHGTSKISRREAKKLADFFGVSVGYLLGL</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>D---NNSKIA</entry><entry>69</entry></row><row><entry /><entry /><entry>D   N+S IA</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>DTTENDSLIA</entry><entry>71</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 581&gt; which encodes the amino acid sequence &lt;SEQ ID 582&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00592" num="00592"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0680(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00593" num="00593"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 21/61 (34%), Positives = 34/61 (55%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MYNRLKELRKDKGLTQADLAKVINTNQSQYGKYENGKTSLSIENSKILADFFGVSIPYLL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MY R++ LR+D   TQ  +A +++ + + Y K E G+ +L  +        + +VSI YLL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MYPRIRNLREDNDFTQKFVANLLSFSHANYAKIERGEVALMADVLVQFYKLYNVSIDYLL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>G</entry><entry>61</entry></row><row><entry /><entry /><entry>G</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>G</entry><entry>61</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 174

A DNA sequence (GBSx0180) was identified in <i>S. agalactiae </i>&lt;SEQ ID 583&gt; which encodes the amino acid sequence &lt;SEQ ID 584&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00594" num="00594"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5278(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 175

A DNA sequence (GBSx0181) was identified in <i>S. agalactiae </i>&lt;SEQ ID 585&gt; which encodes the amino acid sequence &lt;SEQ ID 586&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00595" num="00595"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 60</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3762(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 176

A DNA sequence (GBSx0182) was identified in <i>S. agalactiae </i>&lt;SEQ ID 587&gt; which encodes the amino acid sequence &lt;SEQ ID 588&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00596" num="00596"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.66</entry><entry>Transmembrane</entry><entry>40-56 (33-65)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry>62-78 (59-81)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4864(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8505&gt; and protein &lt;SEQ ID 8506&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00597" num="00597"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 7</entry><entry /></row><row><entry>McG: Discrim Score: −16.96</entry></row><row><entry>GvH: Signal Score (−7.5): −2.95</entry></row><row><entry>     Possible site: 57</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 2 value: −9.66 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="70pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.66</entry><entry>Transmembrane</entry><entry>33-49 (26-58)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.79</entry><entry>Transmembrane</entry><entry>55-71 (52-74)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 10.87</entry><entry>14</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.43</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.4864(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 177

A DNA sequence (GBSx0183) was identified in <i>S. agalactiae </i>&lt;SEQ ID 589&gt; which encodes the amino acid sequence &lt;SEQ ID 590&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00598" num="00598"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3276 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 178

A DNA sequence (GBSx0184) was identified in <i>S. agalactiae </i>&lt;SEQ ID 591&gt; which encodes the amino acid sequence &lt;SEQ ID 592&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00599" num="00599"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3482 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9509&gt; which encodes amino acid sequence &lt;SEQ ID 9510&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00600" num="00600"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA30291 GB: X07371 RepM protein (AA 1-314) [<i>Staphylococcus</i></entry><entry /></row><row><entry><i>aureus</i>]</entry></row><row><entry>Identities = 89/283 (31%), Positives = 145/283 (50%), Gaps = 26/283 (9%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>67</entry><entry>KVSLDNITMTAYIKSKKYLAMKQLIETHLAITVQTAMTDMFRATTGDGIHVVLHMNYDKQ</entry><entry>126</entry><entry /></row><row><entry /><entry /><entry>K+S D +T+   +       +   +     I +   +   F+A     +   +++ YDK</entry></row><row><entry>Sbjct:</entry><entry>42</entry><entry>KLSFDAMTIVGNLNKNSAKKLSDFMSLDPQIRLWDILQTKFKAKA---LQEKVYIEYDKV</entry><entry>98</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>KGQDRKARPFRLEFNPNKLRLVDSEII---DTIIPFLEDISISRADLAFDLFEVDCSEF-</entry><entry>182</entry></row><row><entry /><entry /><entry>K      R  R+EFNPNKL     E++     II ++ED   +R DLAFD FE D S++</entry></row><row><entry>Sbjct:</entry><entry>99</entry><entry>KADTWDRRNMRVEFNPNKL--THDEMLWLKHNIIDYMEDDGFTRLDLAFD-FEDDLSDYY</entry><entry>155</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>-VLEKKGRPTATKEFRSSTGTLETKYLGAPRSEKQVRLYNKKKEQLQNGTDKDKDFASQF</entry><entry>241</entry></row><row><entry /><entry /><entry> + EK  + T    F  +TG  ETKY G+  S + +R+YNKKKE+ +N    D D +++</entry></row><row><entry>Sbjct:</entry><entry>156</entry><entry>ALSEKALKRTV---FFGTTGKAETKYFGSRDSNRFIRIYNKKKERKENA---DVDVSAE-</entry><entry>208</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>KHWWRLEFQLRSRSIDEIFEVI-DTIIFKP--FNLKGLSIETQIYLTALIHDKNIWKKLH</entry><entry>298</entry></row><row><entry /><entry /><entry> H WR+E +L+   +D       D  I KP    L+ L  +  +YL  L+H+++ W +LH</entry></row><row><entry>Sbjct:</entry><entry>209</entry><entry>-HLWRVEIELKRDMVDYWNNCFNDLHILKPAWATLESLKEQAMVYL--LLHEESKWGELH</entry><entry>265</entry></row><row><entry /></row><row><entry>Query:</entry><entry>299</entry><entry>RNTRARYKKILETHQTSDTDYLGLLKDLLKHERPRLENQLAYY</entry><entry>341</entry></row><row><entry /><entry /><entry>RN+R +YK+I++  + S  D   L+K  L      L+ Q+ ++</entry></row><row><entry>Sbjct:</entry><entry>266</entry><entry>RNSRRKYKQIIQ--EISSIDLTDLMKSTLTDNEENLQKQINFW</entry><entry>306</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 179

A DNA sequence (GBSx0185) was identified in <i>S. agalactiae </i>&lt;SEQ ID 593&gt; which encodes the amino acid sequence &lt;SEQ ID 594&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00601" num="00601"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −15.55</entry><entry>Transmembrane</entry><entry>137-153 (133-157)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial membrane --- Certainty = 0.7220 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9511&gt; which encodes amino acid sequence &lt;SEQ ID 9512&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8507&gt; and protein &lt;SEQ ID 8508&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00602" num="00602"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 2</entry><entry /></row><row><entry>McG: Discrim Score: −16.84</entry></row><row><entry>GvH: Signal Score (−7.5): −5.3</entry></row><row><entry>   Possible site: 32</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="224pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 1</entry><entry>value: −15.55</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="42pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="63pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −15.55</entry><entry>Transmembrane</entry><entry>137-153 (133-157)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="203pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><tbody valign="top"><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 10.93</entry><entry>60</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 3.61</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial membrane --- Certainty = 0.7220 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00015" num="00015"><img id="EMI-C00015" he="61.04mm" wi="118.62mm" file="US07939087-20110510-C00015.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00015" attachment-type="cdx" file="US07939087-20110510-C00015.CDX" /><attachment idref="CHEM-US-00015" attachment-type="mol" file="US07939087-20110510-C00015.MOL" /></attachments></chemistry>

SEQ ID 8508 (GBS405) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 171</figref> (lane 4; MW 46 kDa-2 bands) and in <figref idrefs="DRAWINGS">FIG. 177</figref> (lane 7; MW 46 kDa). It was also expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 76</figref> (lane 5; MW 21 kDa).

GBS405-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 218</figref>, lane 8.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 180

A DNA sequence (GBSx0186) was identified in <i>S. agalactiae </i>&lt;SEQ ID 595&gt; which encodes the amino acid sequence &lt;SEQ ID 596&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00603" num="00603"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3406 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00604" num="00604"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA33713 GB:X15669 pre protein (AA 1-494)</entry><entry /></row><row><entry>[<i>Streptococcus agalactiae</i>]</entry></row><row><entry>Identities = 171/402 (42%), Positives = 250/402 (61%),</entry></row><row><entry>Gaps = 46/402 (11%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="right" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="right" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSYVVARMAKYKSGQLTAIYNHNERIFKNHSNKEIDVEKSHLNYELTNRDQAQNYHKQIK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MSY+VARM K K+G L   + HNER+F+ HSNK+I+   +SHLNYELT+RD++ +Y KQIK</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLNYELTDRDRSVSYEKQIK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EHINENRLSTRGVRKDAILCNEWIITSDKTFFDSLDEKQTREFFETAKDYFAEKYGDANI</entry><entry>120</entry></row><row><entry /><entry /><entry>+++NEN++S R +RKDA+LC+EWIITSDK FF+  LDE+QTR FFETAK+YFAE YG++NI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DYVNENKVSNRAIRKDAVLCDEWIITSDKDFFEKLDEEQTRTFFETAKNYFAENYGESNI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>AYARVHLDESTPHMHLGIVPMKNGKLSSKALFGNKEKLVAIQDELPKYLNEHGFNLQRGE</entry><entry>180</entry></row><row><entry /><entry /><entry>AYA VHLDESTPHMH+G+VP +NGKLSSKA+F ++E+L   IQ++LP+Y+++HGF L+RG+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>AYASVHLDESTPHMHMGVVPFENGKLSSKAMF-DREELKHIQEDLPRYMSDHGFELERGK</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>IGSKKKHLETAEFKEKQRLLDNADRKLADKHEELKALDDKISNV-NDTIA----------</entry><entry>229</entry></row><row><entry /><entry /><entry>+ S+ KH   AEFK     ++    +L +K+     +D++   +  NDT A</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>LNSEAKHKTVAEFKRAMADME-LKEELLEKYHAPPFVDERTGELNNDTEAFWHEKEFADM</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>230</entry><entry>-DKESRLKEL---EAKEWDAVGDLKQYELEKQSLAESIEDIKDIELLQLDRIQKEDLVKQ</entry><entry>285</entry></row><row><entry /><entry /><entry> + +S ++E    E  +W      KQY+ E + L  S +  ++D      D    E+L+ +</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>FEVQSPIRETTNQEKMDWLR----KQYQEELKKLESSKKPLED------DLSHLEELLDK</entry><entry>288</entry></row><row><entry /></row><row><entry>Query:</entry><entry>286</entry><entry>SFDGKLKMDKETYNRLFQTASKHASSNAELKRDLVKAQSQNNHLSRELLNHRKTAEKNIK</entry><entry>345</entry></row><row><entry /><entry /><entry>     +K+D E        AS+ AS       +L KA+   N L     NH K+ E  I+</entry></row><row><entry>Sbjct:</entry><entry>289</entry><entry>KTKEYIKIDSE--------ASERAS-------ELSKAEGYINTLE----NHSKSLEAKIE</entry><entry>329</entry></row><row><entry /></row><row><entry>Query:</entry><entry>346</entry><entry>LSQENRKLKDKVKMLDEQVKILNKSLSVWKEKAKEFMPKQVY</entry><entry>387</entry></row><row><entry /><entry /><entry>  + +    +K K    + K LN+S     +  K F+ K+ Y</entry></row><row><entry>Sbjct:</entry><entry>330</entry><entry>CLESDNLQLEKQKATKLEAKALNESELRELKPKKNFLGKEHY</entry><entry>371</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 597&gt; which encodes the amino acid sequence &lt;SEQ ID 598&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00605" num="00605"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>LPXTG motif: 2025-2030</entry><entry /></row><row><entry /></row><row><entry>Possible site: 52</entry></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="70pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.08</entry><entry>Transmembrane</entry><entry>2034-2050 (2030-2053)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood =  −6.05</entry><entry>Transmembrane</entry><entry>    21-37</entry><entry>  (20-39)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5034 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00606" num="00606"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AA003320 GB: AF067776 extracellular matrix binding protein</entry><entry /></row><row><entry>[<i>Abiotrophia defectiva</i>]</entry></row><row><entry>Identities = 362/1396 (25%), Positives = 591/1396 (41%), Gaps = 87/1396 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>636</entry><entry>KAEVKLREAHEATKQAIEKDPWLSPEQKKAQKEKAKARLDEGLKALKAADSLEILKVTEE</entry><entry>695</entry><entry /></row><row><entry /><entry /><entry>+A+  +  A +A   AI+ +  L+ E+K A+K K +A  +  L  +  A      K T</entry></row><row><entry>Sbjct:</entry><entry>636</entry><entry>EAKNAVNNAAKAKNTAIDNNNNLTAEEKAAEKAKVEAAKNATLAGIDQA------KTTAA</entry><entry>689</entry></row><row><entry /></row><row><entry>Query:</entry><entry>696</entry><entry>AFVDKEKNPDSIPNQHKAGTADQARKQALDSLDKEVQKELESIDNDNTLTTDEKAAAKKK</entry><entry>755</entry></row><row><entry /><entry /><entry>    + K    I   +    A  A   AL+   +    ++  I     LT +EK A   +</entry></row><row><entry>Sbjct:</entry><entry>690</entry><entry>RNAAQNKGTTDINAVNPVPVAKPAANAALE---QAAVNKINEISQRPDLTREEKQAFMDQ</entry><entry>746</entry></row><row><entry /></row><row><entry>Query:</entry><entry>756</entry><entry>VNDAYDVARQTAMEANSYEDLTTIKDEFLS---NLPHKQGTPLKDQQSDAIAELEKKQQE</entry><entry>812</entry></row><row><entry /><entry /><entry>V  A D A      A + + +T+ +D+ L+   NLP    TP   +  +A+  + +</entry></row><row><entry>Sbjct:</entry><entry>747</entry><entry>VRTARDAAMAKVASAANNQAVTSARDQGLNAVNNLP----TPAA-KYPEALGHVRQAADA</entry><entry>801</entry></row><row><entry /></row><row><entry>Query:</entry><entry>813</entry><entry>IEKAIEGDKTLPRDEKEKQIADSKERLKSDTQKVKDAKNADAIKKAFEEGKVNIPQAHIP</entry><entry>872</entry></row><row><entry /><entry /><entry>  +AI  +  L  +E+   +        +    +        + KA  +G   I</entry></row><row><entry>Sbjct:</entry><entry>802</entry><entry>KRQAIRDNANLTAEEQADALRQVDAAQTAAEAAINQNHTNATLAKADSDGVKAI------</entry><entry>855</entry></row><row><entry /></row><row><entry>Query:</entry><entry>873</entry><entry>GDLN---KDKEKLLAELKQKADDTEKAIDVDKTLTEDEKKEQKVKTKAELEKAKTDVKNT</entry><entry>929</entry></row><row><entry /><entry /><entry> D+N   + K      L+Q A    +AI+ +  LT++EK +   +    L  AKT V+</entry></row><row><entry>Sbjct:</entry><entry>856</entry><entry>NDINPQPRSKPAANQALEQVAAAKRQAINNNNQLTDEEKAQAIQQVDQALANAKTQVQAA</entry><entry>915</entry></row><row><entry /></row><row><entry>Query:</entry><entry>930</entry><entry>QTREELDKKVPELKKAIEDTHVKGNLEGVKNKAIEDLKKAHTETVAKINGDDTLDKATKE</entry><entry>989</entry></row><row><entry /><entry /><entry>     +++       AI + + +G     K +AI  ++ A      ++ G + L    +</entry></row><row><entry>Sbjct:</entry><entry>916</entry><entry>NDNNGVNQAKTAGTTAINNINPQGTQ---KAQAIAAIEAAEQAKRLELQGRNDLTTEERN</entry><entry>972</entry></row><row><entry /></row><row><entry>Query:</entry><entry>990</entry><entry>AQVKEADKALAAGKDAITKADDADKVSTAVTEHTPKIKAAHKTGDLKKAQVDANTALDKA</entry><entry>1049</entry></row><row><entry /><entry /><entry>  + +      A KDA+ +A +   V+ A      +I+  + T  +K    DA  A+D+A</entry></row><row><entry>Sbjct:</entry><entry>973</entry><entry>NALADLTAKAQAAKDAVNQARNNTGVAGAKDNGVAQIQGINPTAVVKP---DARNAIDQA</entry><entry>1029</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1050</entry><entry>AEKERGEINKDATLTTEDKAKQLKEVETALTKAKDNVKAAKTADAINDARDKGVATIDAV</entry><entry>1109</entry></row><row><entry /><entry /><entry>A  +  E   +  LT E+KA  +K+V+ A   AK  +  A +   +N+A ++G A I A+</entry></row><row><entry>Sbjct:</entry><entry>1030</entry><entry>ARDKEAEFQANTKLTDEEKAAAIKKVQDAARDAKAAIDRAGSNGDVNNAVNQGKAAIQAI</entry><entry>1089</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1110</entry><entry>HKAGQDLGARKSGQVAKLEEAAKATKDKISADPTLTSKEKEEQSKAVDAELKKAIEAVNA</entry><entry>1169</entry></row><row><entry /><entry /><entry>        + K    A ++ AA A K  I+A+  LT +EK    K V+ E  KA  AV+A</entry></row><row><entry>Sbjct:</entry><entry>1090</entry><entry>KALDDSQPSAKDTAKAAIQNAADAKKAAITANNALTQEEKAAAIKQVEDEAAKAQAAVDA</entry><entry>1149</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1170</entry><entry>ADTADKVDDALGEGVTDIKNQHKSGDSIDARREAHGKELDRVAQETKGAIEKDPTLTTEE</entry><entry>1229</entry></row><row><entry /><entry /><entry>+ +   VD A  +G+  I +      ++    +      +D+ A + K  I  D TLT EE</entry></row><row><entry>Sbjct:</entry><entry>1150</entry><entry>SRSKADVDRAKDQGLQKISDV----PAVQPPKLNAIAAVDQAATDKKAVINNDTTLTQEE</entry><entry>1205</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1230</entry><entry>KAKQVKDVDAAKERGMAKLNEAKDADALDKAYGEGVTDIKNQHKSGDPVDARRGLHNKSI</entry><entry>1289</entry></row><row><entry /><entry /><entry>K   ++ VD    +    +N+A     +     +G   I N  ++     A +     ++</entry></row><row><entry>Sbjct:</entry><entry>1206</entry><entry>KEAAIRKVDEEAAKARQAINDATSNADVAAKQAQGTQAINNVPQT----PAAKNAAKAAV</entry><entry>1261</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1290</entry><entry>DEVAQATKDAITADTTLTEAEKETQRGNVDKEATKAKEELAKAKDADALDKAYGDGVTSI</entry><entry>1349</entry></row><row><entry /><entry /><entry>++ A A K AI  D  LT  EK+     VD+E  KA++ +  A     +     +G  +I</entry></row><row><entry>Sbjct:</entry><entry>1262</entry><entry>EQAADAKKQAIENDPNLTRQEKDAAIAKVDQETNKARQAIDAATTNADVTAKQNEGTQAI</entry><entry>1321</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1350</entry><entry>KNQHKSGKGLDVRKDEHKKALEAVAKRVTAEIEADPTLTPEVREQQKAEVQKELELATDK</entry><entry>1409</entry></row><row><entry /><entry /><entry>    ++ K     K + K A+   A+   + IE DP LT E ++  KA+V  E   A +</entry></row><row><entry>Sbjct:</entry><entry>1322</entry><entry>NAVPQTPKA----KTDAKNAVTQAAEDKKSAIENDPNLTREEKDAAKAKVDAEATKAKNA</entry><entry>1377</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1410</entry><entry>IAEAKDADEADKAYGDGVTAIENAHVIGKGIEARKDLAKKDLAEAAAKTKALIIEDKTLT</entry><entry>1469</entry></row><row><entry /><entry /><entry>I  A   D+      +G  AI   + + +  +A+ D AK  + +AA + K  I  D  LT</entry></row><row><entry>Sbjct:</entry><entry>1378</entry><entry>IDAATSNDDETAKQNEGTQAI---NAVPQTPKAKTD-AKNAVTQAADRKKDAIENDPNLT</entry><entry>1433</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1470</entry><entry>DDQRKEQLLGVDTEYAKGIENIDAAKDAAGVDKAYSDGVRDILAQYKEGQNLNDRRNAAK</entry><entry>1529</entry></row><row><entry /><entry /><entry> +++      VD E  K  + IDAA   A V    ++G + I     +       +  AK</entry></row><row><entry>Sbjct:</entry><entry>1434</entry><entry>REEKVAAKAKVDAEAKKAKDAIDAATSNADVTAKQNEGTKAI----NDVPQTPTAKTDAK</entry><entry>1489</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1530</entry><entry>EFLLKEADKVTKLINDDPTLTHDQKVDQINKVEQAKLDAIKSVDDAQTADAINDALGKGI</entry><entry>1589</entry></row><row><entry /><entry /><entry>  + + AD     I  DP LT ++K     KV+     A  ++D A +   +     +G</entry></row><row><entry>Sbjct:</entry><entry>1490</entry><entry>NAVTQAADAKKDAIEKDPNLTREEKDAAKAKVDAEAKKAKDAIDAATSNADVTAKQNEGT</entry><entry>1549</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1590</entry><entry>ENINNQYQHGDGVDVRKATAKGDLEKEAAKVKALIAKDPTLTQADKDKQTAAVDAAKNTA</entry><entry>1649</entry></row><row><entry /><entry /><entry>+ IN+  Q        K  AK  + + A   K  I KDP LT+ +KD   A VDA    A</entry></row><row><entry>Sbjct:</entry><entry>1550</entry><entry>KAINDVPQ----TPTAKTDAKNAVTQAADAKKDAIEKDPNLTREEKDAAKAKVDAEAKKA</entry><entry>1605</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1650</entry><entry>IAAVDKATTTEGINQELGKGITAINKAYRPGEGVKARKEAAKADLEKEAAKVKALITNDP</entry><entry>1709</entry></row><row><entry /><entry /><entry>  A+D AT+   +  +   G  AIN   +        K  AK  + + A   K  I ND</entry></row><row><entry>Sbjct:</entry><entry>1606</entry><entry>KDAIDAATSNADVTAQKDAGKNAINAVPQ----TPTAKTDAKNAVTQAADAKKDAIENDA</entry><entry>1661</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1710</entry><entry>TLTKADK-AKQTEAVAKALKAAIAAVDKATTAEGINQELGKGITAINKAYRPGEGVKARK</entry><entry>1768</entry></row><row><entry /><entry /><entry> LT+ +K A + +  A+A KA   A+D AT+   +  +  +G  AIN   +        K</entry></row><row><entry>Sbjct:</entry><entry>1662</entry><entry>NLTREEKDAAKAKVDAEATKAK-NAIDAATSNADVTAKQNEGTKAINDVPQ----TPTAK</entry><entry>1716</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1769</entry><entry>EAAKADLEREAAKVREAIANDPTLTKADK-AKQTEAVAKALKAAIAAVDKATTAEGINQE</entry><entry>1827</entry></row><row><entry /><entry /><entry>  AK  +++ A   + AI NDP LT+ +K A + +  A+A KA   A+D AT+   +  +</entry></row><row><entry>Sbjct:</entry><entry>1717</entry><entry>TDAKNAVDQAATDKKSAIENDPALTREEKDAAKAKVDAEATKAK-NAIDAATSNADVTAQ</entry><entry>1775</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1828</entry><entry>LGKGITAINKAYRPGEGVEAHKEAAKANLEKVAKETKALISGDRYLSKTEKAVQKQAVEQ</entry><entry>1887</entry></row><row><entry /><entry /><entry>   G  AIN   +        K  AK  +++ A + KA I  D  L+  EK   K  V+</entry></row><row><entry>Sbjct:</entry><entry>1776</entry><entry>KDAGKNAINAVPQ----TPTAKTDAKNAVDQAATDKKAAIENDPALTREEKDAAKAKVDA</entry><entry>1831</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1888</entry><entry>ALAKALGQVEAAKTVEAVKLAENLGTVAIRSAYVAGLAKDTDQATAALNEAKQAAIEALK</entry><entry>1947</entry></row><row><entry /><entry /><entry>   KA   ++AA +   V   ++ G             KD   A      AK  A  A+</entry></row><row><entry>Sbjct:</entry><entry>1832</entry><entry>EAKKAKDAIDAATSNADVTAQKDAG-------------KDAINAVPQTPTAKTDAKNAVD</entry><entry>1878</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1948</entry><entry>QAAAETLAKITTDAKLTEAQKAEQSENVSLALKTAIATVRSAQSIASVKEAKDKGITAIR</entry><entry>2007</entry></row><row><entry /><entry /><entry>QAA +  + I  D  LT  +K      V    K A   + +A S A V   + +G  AI</entry></row><row><entry>Sbjct:</entry><entry>1879</entry><entry>QAATDKKSAIENDPALTREEKDAVKAKVDAEAKKAKDAIDAATSNADVTAKQTEGTQAIN</entry><entry>1938</entry></row><row><entry /></row><row><entry>Query:</entry><entry>2008</entry><entry>AAYVPNKAVAKSSSAN</entry><entry>2023</entry></row><row><entry /><entry /><entry>A  VP    AK+ + N</entry></row><row><entry>Sbjct:</entry><entry>1939</entry><entry>A--VPQTPTAKTDAKN</entry><entry>1952</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00607" num="00607"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 77/396 (19%), Positives = 157/396 (39%), Gaps = 48/396 (12%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="266pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>42</entry><entry>LNYELTNRDQAQNYHKQIKEHINENRLSTRGVRKDAILCNEWIITSDKTFFDSLDEKQTR</entry><entry>101</entry><entry /></row><row><entry /><entry /><entry>L++E+ +  ++QN  K+I + +            D     E +I   K  +++  EK T</entry></row><row><entry>Sbjct:</entry><entry>338</entry><entry>LDFEILH-PRSQNVSKKISKQVEAKPF-------DPASYKEKVIAKLKPVYEATSEKITN</entry><entry>389</entry></row><row><entry /></row><row><entry>Query:</entry><entry>102</entry><entry>EFF--ETAKDYFAEKYGDANIAYARVHLDESTPHMHLGIVPMKNGKLSSKALFG--NKEK</entry><entry>157</entry></row><row><entry /><entry /><entry>+ +  E AKD   +K  +  I+               G V +       +A+    NK</entry></row><row><entry>Sbjct:</entry><entry>390</entry><entry>DAWLDENAKDLQKQKLEEQYIS---------------GKVAISEAGTKQEAIDAAYNKYS</entry><entry>434</entry></row><row><entry /></row><row><entry>Query:</entry><entry>158</entry><entry>LVAIQDELPKYLNEHGFNLQRGEIGSKKKHLETAEFKEKQRLLDN---ADRKLADKHEEL</entry><entry>214</entry></row><row><entry /><entry /><entry>     D LP    +   N +  +   ++  ++T +   K    D       K   K E L</entry></row><row><entry>Sbjct:</entry><entry>435</entry><entry>SQTDPDSLPSQYKQG--NKENEQEKGRQDLIQTRDLTLKAIQEDKWLTEQEKTIQKEEAL</entry><entry>492</entry></row><row><entry /></row><row><entry>Query:</entry><entry>215</entry><entry>KALDDKISNVNDTIADKESRLKELEAKEWDAVGDLKQYE----------LEKQSLAESIE</entry><entry>264</entry></row><row><entry /><entry /><entry>KA +  I +VN T++ ++ + + +  K  +   + K+Y            EK+  A   E</entry></row><row><entry>Sbjct:</entry><entry>493</entry><entry>KAFETGIESVNQTVSLEQLKQRLIVYKASEKDSEKKEYPESIPNQHIPGKEKEVKAAKQE</entry><entry>552</entry></row><row><entry /></row><row><entry>Query:</entry><entry>265</entry><entry>DIKDIELLQLDRIQKEDLVKQSFDGKLKMDKETYNRLFQTASKHASSNAELKRDLVKAQS</entry><entry>324</entry></row><row><entry /><entry /><entry>++K +    L++I ++  +      +     +E   +  Q A K A +  +L+ DL    S</entry></row><row><entry>Sbjct:</entry><entry>553</entry><entry>ELKKLHDTTLEKINQDKWLTPDQQAEQLKQAEVTFKKGQEAIKSAQTLTQLETDLADYVS</entry><entry>612</entry></row><row><entry /></row><row><entry>Query:</entry><entry>325</entry><entry>QNNHLSRELLNHRKTAEKNIKLSQENRKLKDKVKMLDEQVK----ILNKSLSVWKEKAKE</entry><entry>380</entry></row><row><entry /><entry /><entry>+N      + +  K+  K+  +++   KLK+  +   + ++    +  +     KEKAK</entry></row><row><entry>Sbjct:</entry><entry>613</entry><entry>ENEGKGNSIPDKYKSGNKDDLVNKAEVKLKEAHEATKQAIEKDPWLSPEQKKAQKEKAKA</entry><entry>672</entry></row><row><entry /></row><row><entry>Query:</entry><entry>381</entry><entry>FMPKQVYRETLSIINTLNPIGLAKTAIRQVKKMVDS</entry><entry>416</entry></row><row><entry /><entry /><entry> + + +  + L   ++L  + + + A    +K  DS</entry></row><row><entry>Sbjct:</entry><entry>673</entry><entry>RLDEGL--KALKAADSLEILKVTEEAFVDKEKNPDS</entry><entry>706</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 181

A DNA sequence (GBSx0187) was identified in <i>S. agalactiae </i>&lt;SEQ ID 599&gt; which encodes the amino acid sequence &lt;SEQ ID 600&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00608" num="00608"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 42</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2544 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 182

A DNA sequence (GBSx0188) was identified in <i>S. agalactiae </i>&lt;SEQ ID 601&gt; which encodes the amino acid sequence &lt;SEQ ID 602&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00609" num="00609"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2045 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 603&gt; which encodes the amino acid sequence &lt;SEQ ID 604&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00610" num="00610"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2045 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00611" num="00611"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 102/111 (91%), Positives = 107/111 (95%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MDYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQHKMEQIISDIEKLEVFPEVGFDADE</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+DYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQ KMEQIISDIEKLEVFPEVGFDADE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LDYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQRKMEQIISDIEKLEVFPEVGFDADE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KYGSKISKYHSTRGYTLSKDYIVLYHIEEEENRVVIDYLLPTRSDYMKLFK</entry><entry>111</entry></row><row><entry /><entry /><entry>KYGSKI  YHST+GYTLSKDYIVLYHIE EENR+VIDYLLPT+SDY+KLFK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KYGSKIIHYHSTKGYTLSKDYIVLYHIEGEENRIVIDYLLPTQSDYIKLFK</entry><entry>111</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 183

A DNA sequence (GBSx0189) was identified in <i>S. agalactiae </i>&lt;SEQ ID 605&gt; which encodes the amino acid sequence &lt;SEQ ID 606&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00612" num="00612"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1621(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 607&gt; which encodes the amino acid sequence &lt;SEQ ID 608&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00613" num="00613"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1596(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00614" num="00614"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 91/95 (95%), Positives = 93/95 (97%)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVTAEKNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M T +KNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTTVKKNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EKLFKQFQAEINKNIEDVRQGKFYTSEEVRSELGL</entry><entry>95</entry></row><row><entry /><entry /><entry>EKLFKQFQAEINKNIEDVRQGKFYTSEEVR+ELGL</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>EKLFKQFQAEINKNIEDVRQGKFYTSEEVRAELGL</entry><entry>95</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 184

A DNA sequence (GBSx0190) was identified in <i>S. agalactiae </i>&lt;SEQ ID 609&gt; which encodes the amino acid sequence &lt;SEQ ID 610&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00615" num="00615"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 56</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4568(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9513&gt; which encodes amino acid sequence &lt;SEQ ID 9514&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00616" num="00616"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA46375 GB:X65276 ORFA1 [<i>Clostridium acetobutylicum</i>]</entry><entry /></row><row><entry>Identities = 36/91 (39%), Positives = 51/91 (55%)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>MSQIKLTPEELRISAQKYTTGSQSITDVLTVLTQEQAVIDENWDGTAFDSFEAQFNELSP</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>M+QI +TPEEL+  AQ Y    + I   +  +    + I E W G AF ++  Q+N+L</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MAQISVTPEELKSQAQVYIQSKEEIDQAIQKVNSMNSTIAEEWKGQAFQAYLEQYNQLHQ</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>KITQFAQLLEDINQQLLKVADVVEQTDSDIA</entry><entry>92</entry></row><row><entry /><entry /><entry> + QF  LLE +NQQL K AD V + D+  A</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TVVQFENLLESVNQQLNKYADTVAERDAQDA</entry><entry>91</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 185

A DNA sequence (GBSx0191) was identified in <i>S. agalactiae </i>&lt;SEQ ID 611&gt; which encodes the amino acid sequence &lt;SEQ ID 612&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00617" num="00617"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4523(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 186

A DNA sequence (GBSx0192) was identified in <i>S. agalactiae </i>&lt;SEQ ID 613&gt; which encodes the amino acid sequence &lt;SEQ ID 614&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00618" num="00618"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5339(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 187

A DNA sequence (GBSx0193) was identified in <i>S. agalactiae </i>&lt;SEQ ID 615&gt; which encodes the amino acid sequence &lt;SEQ ID 616&gt;. This protein is predicted to be chromosome assembly protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00619" num="00619"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4620(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 188

A DNA sequence (GBSx0194) was identified in <i>S. agalactiae </i>&lt;SEQ ID 617&gt; which encodes the amino acid sequence &lt;SEQ ID 618&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00620" num="00620"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4511(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 189

A DNA sequence (GBSx0195) was identified in <i>S. agalactiae </i>&lt;SEQ ID 619&gt; which encodes the amino acid sequence &lt;SEQ ID 620&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00621" num="00621"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 20</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5249(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 190

A DNA sequence (GBSx0196) was identified in <i>S. agalactiae </i>&lt;SEQ ID 621&gt; which encodes the amino acid sequence &lt;SEQ ID 622&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00622" num="00622"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 14</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3542(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9515&gt; which encodes amino acid sequence &lt;SEQ ID 9516&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 191

A DNA sequence (GBSx0197) was identified in <i>S. agalactiae </i>&lt;SEQ ID 623&gt; which encodes the amino acid sequence &lt;SEQ ID 624&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00623" num="00623"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.3098 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 192

A DNA sequence (GBSx0198) was identified in <i>S. agalactiae </i>&lt;SEQ ID 625&gt; which encodes the amino acid sequence &lt;SEQ ID 626&gt;. This protein is predicted to be rgg protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00624" num="00624"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.3177 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00625" num="00625"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAA26968 GB: M89776 rgg [<i>Streptococcus gordonii</i>]</entry><entry /></row><row><entry>Identities = 74/277 (26%), Positives = 142/277 (50%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>IFREFRLNRQFSLKQVASNELSVSQLSRFERGESDLSLTKFLGALEAIDLSISEFMDRVN</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>I +  R ++  SLK+VA+ ++SV+QLSR+ERG S L++  F   L  + +S++EF    +</entry></row><row><entry>Sbjct:</entry><entry>10</entry><entry>ILKIIRESKNMSLKEVAAGDISVAQLSRYERGISSLTVDSFYSCLRNMSVSLAEFQYVYH</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>KYQKSDQISLMSQMAQYHYQRDVAGLEKMISVEEGKLKKDSSDIRCRLNIVLFRGMICEC</entry><entry>126</entry></row><row><entry /><entry /><entry> Y+++D + L  ++++   + ++  LE +++  E   ++       +LN ++ R  +  C</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>NYREADDVVLSQKLSEAQRENNIVKLESILAGSEAMAQEFPEKKNYKLNTIVIRATLTSC</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>DSSRKMSEEDLCFLSDYLFQKDSWEISDYILIGNLYRYYNTRHICQLVKEVINQKEYYRD</entry><entry>186</entry></row><row><entry /><entry /><entry>+   ++S+ D+ FL+DYLF  + W   +  L  N         +     E+IN+ ++Y +</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>NPDYQVSKGDIEFLTDYLFSVEEWGRYELWLFTNSVNLLTLETLETFASEMINRTQFYNN</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>IYTNRNVVEATLLNVVETLIERRALEEATFFLEKVEALLNNERNAYHRIILLYEKGFLAY</entry><entry>246</entry></row><row><entry /><entry /><entry>+  NR  +   LLNVV   IE   L+ A  FL  ++     E + Y R+++ Y K   +Y</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>LPENRRRIIKMLLNVVSACIENNHLQVAMKFLNYIDNTKIPETDLYDRVLIKYHKALYSY</entry><entry>249</entry></row><row><entry /></row><row><entry>Query:</entry><entry>247</entry><entry>AKGDSRGIQSMKQAIFCFQAIGSKHHVENFQEHFNRV</entry><entry>283</entry></row><row><entry /><entry /><entry>  G+      ++Q +  F+ + S       +E F R+</entry></row><row><entry>Sbjct:</entry><entry>250</entry><entry>KVGNPHARHDIEQCLSTFEYLDSFGVARKLKEQFERI</entry><entry>286</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 627&gt; which encodes the amino acid sequence &lt;SEQ ID 628&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00626" num="00626"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.3792 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00627" num="00627"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 79/275 (28%), Positives = 146/275 (52%), Gaps = 11/275 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>9</entry><entry>REFRLNRQFSLKQVASNELSVSQLSRFERGESDLSLTKFLGALEAIDLSISEFMDRVNKY</entry><entry>68</entry><entry /></row><row><entry /><entry /><entry>R  R  +Q S+  +A   LS SQ+SRFERGES+++ ++ L  L+ ++++I EF+   +K</entry></row><row><entry>Sbjct:</entry><entry>15</entry><entry>RRLRKGKQVSISFLADEYLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVSAHSKT</entry><entry>74</entry></row><row><entry /></row><row><entry>Query:</entry><entry>69</entry><entry>QKSDQISLMSQMAQYHYQRDVAGLEKMISVEEGKLKKDSSDIRCRLNIVLFRGMICECDS</entry><entry>128</entry></row><row><entry /><entry /><entry>  +   +L+SQ  + + +++V  L K++   +    KD    R  +  +LF       DS</entry></row><row><entry>Sbjct:</entry><entry>75</entry><entry>H-THFFTLLSQARKCYAEKNVVKLTKLL---KDYAHKDYE--RTMIKAILF-----SIDS</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>129</entry><entry>SRKMSEEDLCFLSDYLFQKDSWEISDYILIGNLYRYYNTRHICQLVKEVINQKEYYRDIY</entry><entry>188</entry></row><row><entry /><entry /><entry>S   S+E+L  L+DYLF+ + W   + IL+GN  R+ N   +  L KE++    Y</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>SIAPSQEELTRLTDYLFKVEQWGYYEIILLGNCSRFMNYNTLFLLTKEMVASFAYSEQNK</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>189</entry><entry>TNRNVVEATLLNVVETLIERRALEEATFFLEKVEALLNNERNAYHRIILLYEKGFLAYAK</entry><entry>248</entry></row><row><entry /><entry /><entry>TN+ +V    +N +   I+    E + + + K++ LL +E N Y + + LY  G+    +</entry></row><row><entry>Sbjct:</entry><entry>184</entry><entry>TNKMLVTQLSINCLIISIDHSCFEHSRYLINKIDLLLRDELNFYEKTVFLYVHGYYKLKQ</entry><entry>243</entry></row><row><entry /></row><row><entry>Query:</entry><entry>249</entry><entry>GDSRGIQSMKQAIFCFQAIGSKHHVENFQEHFNRV</entry><entry>283</entry></row><row><entry /><entry /><entry> +  G + M+QA+  F+ +G      +++EH+ ++</entry></row><row><entry>Sbjct:</entry><entry>244</entry><entry>EEMSGEEDMRQALQIFKYLGEDSLYYSYKEHYRQI</entry><entry>278</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 193

A DNA sequence (GBSx0199) was identified in <i>S. agalactiae </i>&lt;SEQ ID 629&gt; which encodes the amino acid sequence &lt;SEQ ID 630&gt;. This protein is predicted to be permease. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00628" num="00628"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.07</entry><entry>Transmembrane</entry><entry>217-233 (215-238)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.96</entry><entry>Transmembrane</entry><entry>163-179 (158-185)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.75</entry><entry>Transmembrane</entry><entry>  71-87 (69-91)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.22</entry><entry>Transmembrane</entry><entry>369-385 (356-389)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.15</entry><entry>Transmembrane</entry><entry>279-295 (275-299)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.88</entry><entry>Transmembrane</entry><entry>252-268 (250-270)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.78</entry><entry>Transmembrane</entry><entry>140-156 (139-157)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.56</entry><entry>Transmembrane</entry><entry>343-359 (340-367)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.13</entry><entry>Transmembrane</entry><entry>  40-56 (39-56)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.28</entry><entry>Transmembrane</entry><entry> 94-110 (92-112)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4227(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00629" num="00629"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD36408 GB: AE001788 permease,</entry><entry /></row><row><entry>putative [<i>Thermotoga maritima</i>]</entry></row><row><entry>Identities = 97/396 (24%), Positives = 194/396 (48%),</entry></row><row><entry>Gaps = 15/396 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNINGIKLLSSRAVSKLGDVFYDYGNSTWIASMGGLGQKILGIYQIVELLVSIVLNPFGG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MN N +   S   VS +G   Y    + W+ S  G  + + G++ I   L +I+++PF G</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNRNLLLFASGSFVSLIGTRIYQVALAWWLYSKTGSSEYV-GLFMISSFLPAIIVSPFAG</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>ALADRFQRRKILLITDAICAIM---CFLLSFIGDDKVMVYGLIVANAILAVSNAFSSPAY</entry><entry>117</entry></row><row><entry /><entry /><entry> + DR  RR ++++ D +  ++    FL+ +  +  + +  L++   +++V ++F +PA</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>TVVDRHSRRNMMVVMDILRGVLFMYLFLMEYFSELTMAL--LLIVTVLVSVFDSFFNPAV</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>KSYIPEIVDKADIITYNANLETIVQIISVSSPVLGFLIFNNFGIRITLIVDAITFLISFL</entry><entry>177</entry></row><row><entry /><entry /><entry> S +P++V K +++  N+    +  +  +  P LG L+    G+   +++++++FLIS +</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>DSLLPDLVRKENLVRANSLYRLLKNLSKILGPALGSLLLKVVGLAGVILINSLSFLISGI</entry><entry>177</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>FLYAIKVERVQLSKQEKVAIKNILADIADGFTYIKKEKEIMFFLIIAALLNTFLAMFNYL</entry><entry>237</entry></row><row><entry /><entry /><entry>F   IKVE   L K  K   +N+  DI     YI+  + I+  +++ A++N F    + L</entry></row><row><entry>Sbjct:</entry><entry>178</entry><entry>FEMFIKVEEKHLKKVSKE--RNMWQDIKSALLYIRSVRFILVTILVIAIMNFFTGSMHVL</entry><entry>235</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>LP-FTNSLLKTSGAYATILSISAIGSIIGALIARKI--KSSINSMLSMLVFSSLGVIVMG</entry><entry>294</entry></row><row><entry /><entry /><entry>LP   + L K+   Y T++S+ + G +I   +   I  ++S+ ++   LV   L V V</entry></row><row><entry>Sbjct:</entry><entry>236</entry><entry>LPEHVSKLGKSEWVYGTLMSMLSFGGLIVTFLMATIRTRASVKTLGLNLVGYGLAVFVFA</entry><entry>295</entry></row><row><entry /></row><row><entry>Query:</entry><entry>295</entry><entry>FPSLFELPIWIPYSGSFLFNSLLTMFNIHFFSQVQIRVDEAYMGRVMSTIFTIAIMFMPI</entry><entry>354</entry></row><row><entry /><entry /><entry>         W+ ++  FL     T+FNI+  + +Q+ + E   G++ S I  ++   +P+</entry></row><row><entry>Sbjct:</entry><entry>296</entry><entry>MTGNH----WLMFAMYFLIGIFQTLFNINVITLLQLAIPEEMRGKIFSLISAVSFSLLPV</entry><entry>351</entry></row><row><entry /></row><row><entry>Query:</entry><entry>355</entry><entry>GTLFMTIFSFALSNVSFIVIGCAIAILGGLGFSYSK</entry><entry>390</entry></row><row><entry /><entry /><entry>   F    S  ++     +      I GG+  S  +</entry></row><row><entry>Sbjct:</entry><entry>352</entry><entry>SYGFFGFLSSYVATAHIFITTSMALIAGGVLISLQR</entry><entry>387</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 631&gt; which encodes the amino acid sequence &lt;SEQ ID 632&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00630" num="00630"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.17</entry><entry>Transmembrane</entry><entry>172-188 (161-194)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.07</entry><entry>Transmembrane</entry><entry>220-236 (218-242)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.22</entry><entry>Transmembrane</entry><entry>311-327 (303-329)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.26</entry><entry>Transmembrane</entry><entry> 98-114 (96-118)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry>347-363 (342-370)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.62</entry><entry>Transmembrane</entry><entry>154-170 (151-171)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.25</entry><entry>Transmembrane</entry><entry>284-300 (281-306)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.66</entry><entry>Transmembrane</entry><entry>378-394 (378-396)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.56</entry><entry>Transmembrane</entry><entry>  74-90 (73-92)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.39</entry><entry>Transmembrane</entry><entry>  50-66 (49-66)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4270(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00631" num="00631"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD36408 GB: AE001788 permease, putative [<i>Thermotoga maritima</i>]</entry><entry /></row><row><entry>Identities = 85/345 (24%), Positives = 171/345 (48%), Gaps = 8/345 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>40</entry><entry>SLSLVAVYQSLESVIGVLFNLFGGVIADSFKRKKIIITTNILCGTACLVLSFLTKEQWLV</entry><entry>99</entry><entry /></row><row><entry /><entry /><entry>S   V ++     +  ++ + F G + D   R+ +++  +IL G   + L  +     L</entry></row><row><entry>Sbjct:</entry><entry>36</entry><entry>SSEYVGLFMISSFLPAIIVSPFAGTVVDRHSRRNMMVVMDILRGVLFMYLFLMEYFSELT</entry><entry>95</entry></row><row><entry /></row><row><entry>Query:</entry><entry>100</entry><entry>YAIVL-TNVILAFMSAFSSPSYKAFTKEIVKKDSISQLNSLLETTSTVIKVTVPMVAIFL</entry><entry>158</entry></row><row><entry /><entry /><entry> A++L   V+++   +F +P+  +   ++V+K+++ + NSL      + K+  P +   L</entry></row><row><entry>Sbjct:</entry><entry>96</entry><entry>MALLLIVTVLVSVFDSFFNPAVDSLLPDLVRKENLVRANSLYRLLKNLSKILGPALGSLL</entry><entry>155</entry></row><row><entry /></row><row><entry>Query:</entry><entry>159</entry><entry>YKLLGIHGVLLLDGLSFLIAALLISFILPVNDEVVIKEKVTIREIFNDLKIGFKYVYSHK</entry><entry>218</entry></row><row><entry /><entry /><entry> K++G+ GV+L++ LSFLI+ +   FI    +E  +K+    R ++ D+K    Y+ S +</entry></row><row><entry>Sbjct:</entry><entry>156</entry><entry>LKVVGLAGVILINSLSFLISGIFEMFIKV--EEKHLKKVSKERNMWQDIKSALLYIRSVR</entry><entry>213</entry></row><row><entry /></row><row><entry>Query:</entry><entry>219</entry><entry>SIFIITVLSALVNFFLAAYNLLLPYSNQMFGEISTGLYGTFLTAEAIGGFIGAILSGFVN</entry><entry>278</entry></row><row><entry /><entry /><entry> I +  ++ A++NFF  + ++LLP      G+ S  +YGT ++  + GG I   L   +</entry></row><row><entry>Sbjct:</entry><entry>214</entry><entry>FILVTILVIAIMNFFTGSMHVLLPEHVSKLGK-SEWVYGTLMSMLSFGGLIVTFLMATIR</entry><entry>272</entry></row><row><entry /></row><row><entry>Query:</entry><entry>279</entry><entry>KELSSMRLILFLSLSGLMLMLAPPFYIMFHNAIILALSPALFSLFLSIFNIQFFSLVQKD</entry><entry>338</entry></row><row><entry /><entry /><entry>   S   L L L   GL + +    + M  N  ++     L  +F ++FNI   +L+Q</entry></row><row><entry>Sbjct:</entry><entry>273</entry><entry>TRASVKTLGLNLVGYGLAVFV----FAMTGNHWLMFAMYFLIGIFQTLFNINVITLLQLA</entry><entry>328</entry></row><row><entry /></row><row><entry>Query:</entry><entry>339</entry><entry>VDNDFLGRVFGIIFTITILFMPIGTGFFSVALNPNNSFNLFIIGS</entry><entry>383</entry></row><row><entry /><entry /><entry>+  +  G++F +I  ++   +P+  GFF    +   + ++FI  S</entry></row><row><entry>Sbjct:</entry><entry>329</entry><entry>IPEEMRGKIFSLISAVSFSLLPVSYGFFGFLSSYVATAHIFITTS</entry><entry>373</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00632" num="00632"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 136/379 (35%), Positives = 229/379 (59%), Gaps = 6/379 (1%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>8</entry><entry>LLSSRAVSKLGDVFYDYGNSTWIASMGGLGQKILGIYQIVELLVSIVLNPFGGALADRFQ</entry><entry>67</entry><entry /></row><row><entry /><entry /><entry>L+ S+ + ++GDV +D+ N+T++A +      ++ +YQ +E ++ ++ N FGG +AD F+</entry></row><row><entry>Sbjct:</entry><entry>11</entry><entry>LVYSKVIYRIGDVMFDFANNTFLAGLNPASLSLVAVYQSLESVIGVLFNLFGGVIADSFK</entry><entry>70</entry></row><row><entry /></row><row><entry>Query:</entry><entry>68</entry><entry>RRKILLITDAICAIMCFLLSFIGDDKVMVYGLIVANAILAVSNAFSSPAYKSYIPEIVDK</entry><entry>127</entry></row><row><entry /><entry /><entry>R+KI++ T+ +C   C +LSF+  ++ +VY +++ N ILA  +AFSSP+YK++  EIV K</entry></row><row><entry>Sbjct:</entry><entry>71</entry><entry>RKKIIITTNILCGTACLVLSFLTKEQWLVYAIVLTNVILAFMSAFSSPSYKAFTKEIVKK</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>128</entry><entry>ADIITYNANLETIVQIISVSSPVLGFLIFNNFGIRITLIVDAITFLISFLFLYAIKVERV</entry><entry>187</entry></row><row><entry /><entry /><entry>  I   N+ LET   +I V+ P++   ++   GI   L++D ++FLI+ L +  I</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>DSISQLNSLLETTSTVIKVTVPMVAIFLYKLLGIHGVLLLDGLSFLIAALLISFILPVND</entry><entry>190</entry></row><row><entry /></row><row><entry>Query:</entry><entry>188</entry><entry>QLSKQEKVAIKNILADIADGFTYIKKEKEIMFFLIIAALLNTFLAMFNYLLPFTNSLLK-</entry><entry>246</entry></row><row><entry /><entry /><entry>++  +EKV I+ I  D+  GF Y+   K I    +++AL+N FLA +N LLP++N +</entry></row><row><entry>Sbjct:</entry><entry>191</entry><entry>EVVIKEKVTIREIFNDLKIGFKYVYSHKSIFIITVLSALVNFFLAAYNLLLPYSNQMFGE</entry><entry>250</entry></row><row><entry /></row><row><entry>Query:</entry><entry>247</entry><entry>-TSGAYATILSISAIGSIIGALIARKIKSSINSMLSMLVFSSLGVIVMGFPS---LFELP</entry><entry>302</entry></row><row><entry /><entry /><entry> ++G Y T L+  AIG  IGA+++  +   ++SM  +L  S  G+++M  P    +F</entry></row><row><entry>Sbjct:</entry><entry>251</entry><entry>ISTGLYGTFLTAEAIGGFIGAILSGFVNKELSSMRLILFLSLSGLMLMLAPPFYIMFHNA</entry><entry>310</entry></row><row><entry /></row><row><entry>Query:</entry><entry>303</entry><entry>IWIPYSGSFLFNSLLTMFNIHFFSQVQIRVDEAYMGRVMSTIFTIAIMFMPIGTLFMTIF</entry><entry>362</entry></row><row><entry /><entry /><entry>I +  S + LF+  L++FNI FFS VQ  VD  ++GRV   IFTI I+FMPIGT F ++</entry></row><row><entry>Sbjct:</entry><entry>311</entry><entry>IILALSPA-LFSLFLSIFNIQFFSLVQKDVDNDFLGRVFGIIFTITILFMPIGTGFFSVA</entry><entry>369</entry></row><row><entry /></row><row><entry>Query:</entry><entry>363</entry><entry>SFALSNVSFIVIGCAIAIL</entry><entry>381</entry></row><row><entry /><entry /><entry>    ++ +  +IG  I  L</entry></row><row><entry>Sbjct:</entry><entry>370</entry><entry>LNPNNSFNLFIIGSCITTL</entry><entry>388</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 194

A DNA sequence (GBSx0200) was identified in <i>S. agalactiae </i>&lt;SEQ ID 633&gt; which encodes the amino acid sequence &lt;SEQ ID 634&gt;. This protein is predicted to be membrane permease OpuCD. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00633" num="00633"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.68</entry><entry>Transmembrane</entry><entry> 91-107 (88-110)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>  15-31 (9-37)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.72</entry><entry>Transmembrane</entry><entry>  72-88 (72-88)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.19</entry><entry>Transmembrane</entry><entry>124-140 (123-142)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3272(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8509&gt; which encodes amino acid sequence &lt;SEQ ID 8510&gt; was also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00634" num="00634"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 1</entry><entry /></row><row><entry>McG: Discrim Score: −10.69</entry></row><row><entry>GvH: Signal Score (−7.5): −3.79</entry></row><row><entry>     Possible site: 39</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 5 value: −9.02 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.02</entry><entry>Transmembrane</entry><entry>  35-51 (25-53)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.68</entry><entry>Transmembrane</entry><entry>151-167 (148-170)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.30</entry><entry>Transmembrane</entry><entry>  75-91 (69-97)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.72</entry><entry>Transmembrane</entry><entry>132-148 (132-148)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.19</entry><entry>Transmembrane</entry><entry>184-200 (183-202)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 2.17</entry><entry>58</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.30</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.4609(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00635" num="00635"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF91342 GB: AF249729 membrane permease OpuCD</entry><entry /></row><row><entry>[<i>Listeria monocytogenes</i>]</entry></row><row><entry>Identities = 104/154 (67%), Positives = 133/154 (85%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>IANVIQTIPSLAMISIIMLGLGLGIKTVVATVFLYSLLPIITNTYTGIRNVDSDLLDAAK</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>IAN+IQTIP+LAM++++ML +GLG  TVV ++FLYSLLPI+ NTYTGIRNVD  LL++ K</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>IANIIQTIPALAMLAVLMLIMGLGTNTVVLSLFLYSLLPILKNTYTGIRNVDGALLESGK</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>GMGMTKRQRLFMVELPLSISVIMAGLRNALVVAIGITAIGAFVGGGGLGDIIIRGTNATN</entry><entry>122</entry></row><row><entry /><entry /><entry> MGMTK Q L ++E+PL++SVIMAG+RNALV+AIG+ AIG FVG GGLGDII+RGTNATN</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>AMGMTKWQVLRLIEMPLALSVIMAGIRNALVIAIGVAAIGTFVGAGGLGDIIVRGTNATN</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>GGAIILAGSLPTALMAIFSDLILGGIQRMLEPRK</entry><entry>156</entry></row><row><entry /><entry /><entry>G AIILAG++PTA+MAI +D++LG ++R L P K</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>GTAIILAGAIPTAVMAILADVLLGWVERTLNPVK</entry><entry>213</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 635&gt; which encodes the amino acid sequence &lt;SEQ ID 636&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00636" num="00636"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.24</entry><entry>Transmembrane</entry><entry>  39-55 (31-59)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.17</entry><entry>Transmembrane</entry><entry>190-206 (188-211)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.62</entry><entry>Transmembrane</entry><entry> 93-109 (75-110)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.66</entry><entry>Transmembrane</entry><entry>  76-92 (75-92)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.87</entry><entry>Transmembrane</entry><entry>221-237 (220-237)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.44</entry><entry>Transmembrane</entry><entry>168-184 (165-184)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4694(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00637" num="00637"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAD45530 GB: AF162656 choline transporter [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 344/508 (67%), Positives = 425/508 (82%), Gaps = 2/508 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>13</entry><entry>MPSLFVTFQNRFNEWLAALGEHLQISLLSLMIALLIGVPLAALLSRSKRWSDIMLQVTGV</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>M +L  TFQ+RF++WL AL +HLQ+SLL+L++A+L+ +PLA  L   ++ +D +LQ+ G+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTNLIATFQDRFSDWLTALSQHLQLSLLTLLLAILLAIPLAVFLRYHEKLADWVLQIAGI</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>FQTIPSLALLGLFIPLMGIGTLPAVTALVIYAIFPILQNTITGLNGIDPSLVEAGIAFGM</entry><entry>132</entry></row><row><entry /><entry /><entry>FQTIPSLALLGLFIPLMGIGTLPA+TALVIYAIFPILQNTITGL GIDP+L EAGIAFGM</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>FQTIPSLALLGLFIPLMGIGTLPALTALVIYAIFPILQNTITGLKGIDPNLQEAGIAFGM</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>133</entry><entry>TKWERLKTFEIPIAMPVIMSGVRTSAVMIIGTATLASLIGAGGLGSFILLGIDRNNANLI</entry><entry>192</entry></row><row><entry /><entry /><entry>T+WERLK FEIP+AMPVIMSG+RT+AV+IIGTATLA+LIGAGGLGSFILLGIDRNNA+LI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>TRWERLKKFEIPLAMPVIMSGIRTAAVLIIGTATLAALIGAGGLGSFILLGIDRNNASLI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>193</entry><entry>LIGAISSALLAIIFNSLLQYLEKASLRRIMISFGITLLALLASYTPMALSQFSKGKDTVV</entry><entry>252</entry></row><row><entry /><entry /><entry>LIGA+SSA+LAI FN LL+ +EKA LR I   F +  L L  SY+P  L Q  K K+ +V</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LIGALSSAVLAIAFNFLLKVMEKAKLRTIFSGFALVALLLGLSYSPALLVQ--KEKENLV</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>253</entry><entry>IAGKLGAEPDILINLYKELIEDQSDISVELKSNFGKTSFLYEALKSGDIDMYPEFTGTIT</entry><entry>312</entry></row><row><entry /><entry /><entry>IAGK+G EP+IL N+YK LIE+ + ++  +K NFGKTSFLYEALK GDID+YPEFTGT+T</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>IAGKIGPEPEILANMYKLLIEENTSMTATVKPNFGKTSFLYEALKKGDIDIYPEFTGTVT</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>313</entry><entry>SSLLRDKPPLSNDPKQVYEDAKKGIAKQDKLTLLKPFAYQNTYAVAMPEKLAKEYQIETI</entry><entry>372</entry></row><row><entry /><entry /><entry> SLL+  P +S++P+QVY+ A+ GIAKQD L  LKP +YQNTYAVA+P+K+A+EY ++TI</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>ESLLQPSPKVSHEPEQVYQVARDGIAKQDHLAYLKPMSYQNTYAVAVPKKIAQEYGLKTI</entry><entry>358</entry></row><row><entry /></row><row><entry>Query:</entry><entry>373</entry><entry>SDLKAHADTLKAGFTLEFKDRADGYKGMQSQYGLQLSVATMEPALRYQAIQSGDIQVTDA</entry><entry>432</entry></row><row><entry /><entry /><entry>SDLK     LKAGFTLEF DR DG KG+QS YGL L+VAT+EPALRYQAIQSGDIQ+TDA</entry></row><row><entry>Sbjct:</entry><entry>359</entry><entry>SDLKKVEGQLKAGFTLEFNDREDGNKGLQSMYGLNLNVATIEPALRYQAIQSGDIQITDA</entry><entry>418</entry></row><row><entry /></row><row><entry>Query:</entry><entry>433</entry><entry>YSTDAEITKYHLKVLKDDKQLFPPYQGAPLMKTSLLTKHPELKGILNQLAGKITEKEMQD</entry><entry>492</entry></row><row><entry /><entry /><entry>YSTDAE+ +Y L+VL+DDKQLFPPYQGAPLMK +LL KHPEL+ +LN LAGKITE +M</entry></row><row><entry>Sbjct:</entry><entry>419</entry><entry>YSTDAELERYDLQVLEDDKQLFPPYQGAPLMKEALLKKHPELERVLNTLAGKITESQMSQ</entry><entry>478</entry></row><row><entry /></row><row><entry>Query:</entry><entry>493</entry><entry>MNYEVSVKGADANKVARDYLLKTGLIQK</entry><entry>520</entry></row><row><entry /><entry /><entry>+NY+V V+G  A +VA+++L + GL++K</entry></row><row><entry>Sbjct:</entry><entry>479</entry><entry>LNYQVGVEGKSAKQVAKEFLQEQGLLKK</entry><entry>506</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00638" num="00638"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 53/148 (35%), Positives = 93/148 (62%), Gaps = 1/148 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>IANVIQTIPSLAMISIIMLGLGLGIKTVVATVFLYSLLPIITNTYTGIRNVDSDLLDAAK</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>+  V QTIPSLA++ + +  +G+G    V  + +Y++ PI+ NT TG+  +D  L++A</entry></row><row><entry>Sbjct:</entry><entry>69</entry><entry>VTGVFQTIPSLALLGLFIPLMGIGTLPAVTALVIYAIFPILQNTITGLNGIDPSLVEAGI</entry><entry>128</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>GMGMTKRQRLFMVELPLSISVIMAGLRNALVVAIGITAIGAFVGGGGLGDIIIRGTNATN</entry><entry>122</entry></row><row><entry /><entry /><entry>  GMTK +RL   E+P+++ VIM+G+R + V+ IG   + + +G GGLG  I+ G +  N</entry></row><row><entry>Sbjct:</entry><entry>129</entry><entry>AFGMTKWERLKTFEIPIAMPVIMSGVRTSAVMIIGTATLASLIGAGGLGSFILLGIDRNN</entry><entry>188</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>GGAIILAGSLPTALMAIFSDLILGGIQR</entry><entry>150</entry></row><row><entry /><entry /><entry>   +IL G++ +AL+AI  + +L  +++</entry></row><row><entry>Sbjct:</entry><entry>189</entry><entry>AN-LILIGAISSALLAIIFNSLLQYLEK</entry><entry>215</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 195

A DNA sequence (GBSx0201) was identified in <i>S. agalactiae </i>&lt;SEQ ID 637&gt; which encodes the amino acid sequence &lt;SEQ ID 638&gt;. This protein is predicted to be choline transporter-related. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00639" num="00639"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.03</entry><entry>Transmembrane</entry><entry>306-322 (306-327)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2211(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9517&gt; which encodes amino acid sequence &lt;SEQ ID 9518&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00640" num="00640"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB15386 GB: Z99121 glycine betaine/carnitine/choline ABC</entry><entry /></row><row><entry>transporter (osmoprotectant-binding protein) [<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 168/303 (55%), Positives = 224/303 (73%), Gaps = 1/303 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>LKKSHFLQIFTLCLALLTISGCQLTDTKKSGHTTIKVAAQSSTESSIMANIITELIHHEL</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+ K  +L  F L   +L + GC L     +   TIK+ AQS TES I+AN+I +LI H+</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTKIKWLGAFALVFVML-LGGCSLPGLGGASDDTIKIGAQSMTESEIVANMIAQLIEHDT</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>GYNTTLISNLGSSTVTHQALLRGDADIAATRYTGTDITGTLGLKAVKDPKEASKIVKTEF</entry><entry>121</entry></row><row><entry /><entry /><entry>  NT L+ NLGS+ V HQA+L GD DI+ATRY+GTD+T TLG +A KDPK+A  IV+ EF</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>DLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEF</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>QKRYNQTWYPTYGFSDTYAFMVTKEFARQNKITKISDLKKLSTTMKAGVDSSWMNREGDG</entry><entry>181</entry></row><row><entry /><entry /><entry>QKR++  W+ +YGF +TYAF VTK+FA +  I  +SDLKK ++  K GVD++W+ R+GDG</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>QKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDG</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>YTDFAKTYGFEFSHIYPMQIGLVYDAVESNKMQSVLGYSTDGRISSYDLEILRDDKKFFP</entry><entry>241</entry></row><row><entry /><entry /><entry>Y  F  TYGFEF   YPMQIGLVYDAV++ KM +VL YSTDGRI +YDL+IL+DDK+FFP</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>YKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFP</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>PYEASMVVNNSIIKKDPKLKKLLHRLDGKINLKTMQNLNYMVDDKLLEPSVVAKQFLEKN</entry><entry>301</entry></row><row><entry /><entry /><entry>PY+ S V+   ++K+ P+L+ ++++L G+I+ +TMQ LNY VD KL EPSVVAK+FLEK+</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>PYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKH</entry><entry>299</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>HYF</entry><entry>304</entry></row><row><entry /><entry /><entry>HYF</entry></row><row><entry>Sbjct:</entry><entry>300</entry><entry>HYF</entry><entry>302</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

A related GBS gene &lt;SEQ ID 8511&gt; and protein &lt;SEQ ID 8512&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00641" num="00641"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: 22 Crend: 5</entry><entry /></row><row><entry>McG: Discrim Score: 10.26</entry></row><row><entry>GvH: Signal Score (−7.5): −4.19</entry></row><row><entry>Possible site: 44</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="49pt" align="left" /><colspec colname="4" colwidth="231pt" align="left" /><colspec colname="5" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 0</entry><entry>value: 8.65</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="1"><colspec colname="1" colwidth="441pt" align="left" /><tbody valign="top"><row><entry>   PERIPHERAL Likelihood = 8.65 66</entry></row><row><entry>modified ALOM score: −2.23</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00016" num="00016"><img id="EMI-C00016" he="132.08mm" wi="124.54mm" file="US07939087-20110510-C00016.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00016" attachment-type="cdx" file="US07939087-20110510-C00016.CDX" /><attachment idref="CHEM-US-00016" attachment-type="mol" file="US07939087-20110510-C00016.MOL" /></attachments></chemistry>

SEQ ID 8512 (GBS23) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 14</figref> (lane 8; MW 35 kDa).

The GBS23-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 194</figref>, lane 9) and used to immunise mice. The resulting antiserum was used for Western blot (<figref idrefs="DRAWINGS">FIG. 251</figref>). These tests confirm that the protein is immunoaccessible on GBS bacteria.

EXAMPLE 196

A DNA sequence (GBSx0202) was identified in <i>S. agalactiae </i>&lt;SEQ ID 639&gt; which encodes the amino acid sequence &lt;SEQ ID 640&gt;. This protein is predicted to be membrane permease OpuCB (opuBB). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00642" num="00642"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 34</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><colspec colname="6" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −9.66</entry><entry>Transmembrane</entry><entry>25-41 (18-45)</entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −7.96</entry><entry>Transmembrane</entry><entry>182-198 (174-202)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.83</entry><entry>Transmembrane</entry><entry>61-77 (57-95)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.09</entry><entry>Transmembrane</entry><entry>78-94 (78-95)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.22</entry><entry>Transmembrane</entry><entry>134-150 (134-150)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.4864 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00643" num="00643"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF91340 GB: AF249729 membrane permease OpuCB [<i>Listeria</i></entry><entry /></row><row><entry><i>monocytogenes</i>]</entry></row><row><entry>Identities = 121/208 (58%), Positives = 160/208 (76%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVNFLSQYGMQILVKTWEQVYISFFAIALGIAIAVPLGVVLTRFPKVAKIIIAIASMLQT</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+V F  + G  +LV+TW+ ++IS  A+ LGIA+AVP G++LTR PKVA  +I + S+LQT</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>IVTFFQENGHNLLVQTWQHLFISLSAVILGIAVAVPTGILLTRSPKVANFVIGVVSVLQT</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>IPSLALLALMIPLFGIGKIPAIVALFIYSLLPILRNTYIGMNNVNPTLKDCAKGMGMKPI</entry><entry>120</entry></row><row><entry /><entry /><entry>+PSLA+LA +IP  G+G +PAI+ALFIY+LLPILRNT+IG+  V+  L +  +GMGM</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>VPSLAILAFIIPFLGVGTLPAIIALFIYALLPILRNTFIGVRGVDKNLIESGRGMGMTNW</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>QSIFQVELPLATPIIMAGIRLSTIYVIAWATLASYIGAGGLGDLIFSGLNLFQSKLILGG</entry><entry>180</entry></row><row><entry /><entry /><entry>Q I  VE+P +  +IMAGIRLS +YVIAWATLASYIGAGGLGD IF+GLNL++  LILGG</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>QLIVNVEIPNSISVIMAGIRLSAVYVIAWATLASYIGAGGLGDFIFNGLNLYRPDLILGG</entry><entry>183</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>TIPVIILSLIIDYLLGLLETALTPRTTR</entry><entry>208</entry></row><row><entry /><entry /><entry> IPV IL+L++++ LG LE  LTP+  R</entry></row><row><entry>Sbjct:</entry><entry>184</entry><entry>AIPVTILALVVEFALGKLEYRLTPKAIR</entry><entry>211</entry></row></tbody></tgroup></table></tables>

A related GBS gene &lt;SEQ ID 8513&gt; and protein &lt;SEQ ID 8514&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00644" num="00644"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 0</entry><entry /></row><row><entry>McG: Discrim Score: −9.08</entry></row><row><entry>GvH: Signal Score (−7.5): −1.86</entry></row><row><entry>Possible site: 37</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 5</entry><entry>value: −8.60</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −8.60</entry><entry>Transmembrane</entry><entry>  25-41 (18-45)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −7.96</entry><entry>Transmembrane</entry><entry>182-198 (174-202)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.83</entry><entry>Transmembrane</entry><entry>  61-77 (57-95)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −4.09</entry><entry>Transmembrane</entry><entry>  78-94 (78-95)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −1.22</entry><entry>Transmembrane</entry><entry>134-150 (134-150)</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="14pt" align="center" /><colspec colname="4" colwidth="133pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 2.70</entry><entry>156</entry><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.22</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.4439 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00017" num="00017"><img id="EMI-C00017" he="74.51mm" wi="118.62mm" file="US07939087-20110510-C00017.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00017" attachment-type="cdx" file="US07939087-20110510-C00017.CDX" /><attachment idref="CHEM-US-00017" attachment-type="mol" file="US07939087-20110510-C00017.MOL" /></attachments></chemistry>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 197

A DNA sequence (GBSx0203) was identified in <i>S. agalactiae </i>&lt;SEQ ID 641&gt; which encodes the amino acid sequence &lt;SEQ ID 642&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00645" num="00645"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3531 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00646" num="00646"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAF91339 GB: AF249729 ATPase OpuCA [<i>Listeria monocytogenes</i>]</entry><entry /></row><row><entry>Identities = 230/380 (60%), Positives = 298/380 (77%), Gaps = 4/380 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>IIEYQNINKVY-GENVAVEDINLKIYPGDFVCFIGTSGSGKTTLMRMVNHMLKPTNGTLL</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>+++++++ K Y G   AV D+ L I  G+FVCFIG SG GKTT M+M+N +++PT G +</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MLKFEHVTKTYKGGKKAVNDLTLNIDKGEFVCFIGPSGCGKTTTMKMINRLIEPTEGKIF</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>FKGKDISTINPIELRRRIGYVIQNIGLMPHMTIYENIVLVPKLLKWSEEAKRAKARELIK</entry><entry>124</entry></row><row><entry /><entry /><entry>   KDI   +P++LRR IGYVIQ IGLMPHMTI ENIVLVPKLLKWSEE K+ +A+ELIK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>INDKDIMAEDPVKLRRSIGYVIQQIGLMPHMTIRENIVLVPKLLKWSEEKKQERAKELIK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LVELPEEYLDRYPSELSGGQQQRIGVIRALAADQDIILMDEPFGALDPITREGIQDLVKS</entry><entry>184</entry></row><row><entry /><entry /><entry>LV+LPEE+LDRYP ELSGGQQQRIGV+RALAA+Q++ILMDEPFGALDPITR+ +Q+  K+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LVDLPEEFLDRYPYELSGGQQQRIGVLRALAAEQNLILMDEPFGALDPITRDSLQEEFKN</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>LQEEMGKTIILVTHDMDEALKLATKIIVMDNGKMVQEGTPNDLLHHPATSFVEQMIGEER</entry><entry>244</entry></row><row><entry /><entry /><entry>LQ+E+GKTII VTHDMDEA+KLA +I++M +G++VQ  TP+++L +PA SFVE  IG++R</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LQKELGKTIIFVTHDMDEAIKLADRIVIMKDGEIVQFDTPDEILRNPANSFVEDFIGKDR</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>LLHAQADITPVKQIMLNNPVSITAEKTLTEAITLMRQKRVDSLLVTDNGKLI-GFIDLES</entry><entry>303</entry></row><row><entry /><entry /><entry>L+ A+ D+T V QIM  NPVSITA+K+L  AIT+M++KRVD+LLV D G ++ GFID+E</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>LIEAKPDVTQVAQIMNTNPVSITADKSLQAAITVMKEKRVDTLLVVDEGNVLKGFIDVEQ</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>304</entry><entry>LSSKYKKDRLVSDILKHTDFYVMEDDLLRNTAERILKLGLKYAPVVDHENNLKGIVTRAS</entry><entry>363</entry></row><row><entry /><entry /><entry>+    +    V DI++   FYV ED LLR+T +RILK G KY PVVD +  L GIVTRAS</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>IDLNRRTATSVMDIIEKNVFYVYEDTLLRDTVQRILKRGYKYIPVVDKDKRLVGIVTRAS</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>364</entry><entry>LVDMLYDIIWGDTE--TEDQ</entry><entry>381</entry></row><row><entry /><entry /><entry>LVD++YD IWG  E  TE+Q</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>LVDIVYDSIWGTLEDATENQ</entry><entry>380</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 643&gt; which encodes the amino acid sequence &lt;SEQ ID 644&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00647" num="00647"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3619(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00648" num="00648"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 102/237 (43%), Positives = 165/237 (69%), Gaps = 1/237 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>6</entry><entry>IIEYQNINKVYGENVAVEDINLKIYPGDFVCFIGTSGSGKTTLMRMVNHMLKPTNGTLLF</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>+I + N++K +G+   +++   +I   +F   +G SGSGKTTL++M+N +++P++G +L</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MIRFNNVSKTFGQTKVLQEQTFQINDREFFVLVGPSGSGKTTLLKMINCLIEPSSGDILL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>KGKDISTINPIELRRRIGYVIQNIGLMPHMTIYENIVLVPKLLKWSEEAKRAKARELIKL</entry><entry>125</entry></row><row><entry /><entry /><entry>     + ++  E+R  IGYV+Q I L P++T+ ENI ++P++ +WS E  R K  EL+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>NNVPQTELDLREMRLSIGYVLQQIALFPNLTVAENIAIIPEMKQWSAEEIRQKTEELLDK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>VELP-EEYLDRYPSELSGGQQQRIGVIRALAADQDIILMDEPFGALDPITREGIQDLVKS</entry><entry>184</entry></row><row><entry /><entry /><entry>V LP ++YLDRYPS+LSGG+QQRIG++RA+ +   I+LMDEPF ALDPI+R+ +Q+L+ S</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VGLPAKDYLDRYPSDLSGGEQQRIGIVRAIISHPKILLMDEPFSALDPISRKQLQELMLS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>LQEEMGKTIILVTHDMDEALKLATKIIVMDNGKMVQEGTPNDLLHHPATSFVEQMIG</entry><entry>241</entry></row><row><entry /><entry /><entry>L +E   TI+ VTHD+DEA+KL  ++ +++ G++VQ   P  +  HPA +FV  + G</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LHKEFDMTIVFVTHDIDEAIKLGDRVAILNEGEIVQLDRPEMIKTHPANAFVVNLFG</entry><entry>237</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 198

A repeated DNA sequence (GBSx0212) was identified in <i>S. agalactiae </i>&lt;SEQ ID 645&gt; which encodes the amino acid sequence &lt;SEQ ID 646&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00649" num="00649"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4736(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 199

A DNA sequence (GBSx0213) was identified in <i>S. agalactiae </i>&lt;SEQ ID 647&gt; which encodes the amino acid sequence &lt;SEQ ID 648&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00650" num="00650"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="77pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.06</entry><entry>Transmembrane</entry><entry>18-34 (18-34)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1426(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty= 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8515&gt; and protein &lt;SEQ ID 8516&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00651" num="00651"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: 20 Crend: 5</entry><entry /></row><row><entry>       Sequence Pattern: CQMN</entry></row><row><entry>SRCFLG: 0</entry></row><row><entry>McG: Length of UR: 19</entry></row><row><entry>     Peak Value of UR: 2.60</entry></row><row><entry>     Net Charge of CR: 3</entry></row><row><entry>McG: Discrim Score: 7.77</entry></row><row><entry>GvH: Signal Score (−7.5): −4.89</entry></row><row><entry>     Possible site: 25</entry></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry>Amino Acid Composition: calculated from 21</entry></row><row><entry>ALOM program count: 0 value: 13.21 threshold: 0.0</entry></row><row><entry>PERIPHERAL Likelihood = 13.21 115</entry></row><row><entry>modified ALOM score: −3.14</entry></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<chemistry id="CHEM-US-00018" num="00018"><img id="EMI-C00018" he="52.07mm" wi="118.62mm" file="US07939087-20110510-C00018.TIF" alt="embedded image" img-content="chem" img-format="tif" /><attachments><attachment idref="CHEM-US-00018" attachment-type="cdx" file="US07939087-20110510-C00018.CDX" /><attachment idref="CHEM-US-00018" attachment-type="mol" file="US07939087-20110510-C00018.MOL" /></attachments></chemistry>

SEQ ID 8516 (GBS389) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 74</figref> (lane 6; MW 18 kDa).

The GBS389-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 214</figref>, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 313</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 200

A DNA sequence (GBSx0214) was identified in <i>S. agalactiae </i>&lt;SEQ ID 649&gt; which encodes the amino acid sequence &lt;SEQ ID 650&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00652" num="00652"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 19</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3766 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 201

A DNA sequence (GBSx0215) was identified in <i>S. agalactiae </i>&lt;SEQ ID 651&gt; which encodes the amino acid sequence &lt;SEQ ID 652&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00653" num="00653"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 46</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial cytoplasm --- Certainty = 0.3882 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>               bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 202

A DNA sequence (GBSx0216) was identified in <i>S. agalactiae </i>&lt;SEQ ID 653&gt; which encodes the amino acid sequence &lt;SEQ ID 654&gt;. This protein is predicted to be lectin, alpha subunit precursor. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00654" num="00654"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0653 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 203

A DNA sequence (GBSx0217) was identified in <i>S. agalactiae </i>&lt;SEQ ID 655&gt; which encodes the amino acid sequence &lt;SEQ ID 656&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00655" num="00655"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.6569(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 204

A DNA sequence (GBSx0218) was identified in <i>S. agalactiae </i>&lt;SEQ ID 657&gt; which encodes the amino acid sequence &lt;SEQ ID 658&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00656" num="00656"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5736(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 205

A DNA sequence (GBSx0219) was identified in <i>S. agalactiae </i>&lt;SEQ ID 659&gt; which encodes the amino acid sequence &lt;SEQ ID 660&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00657" num="00657"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 52</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −13.11</entry><entry>Transmembrane</entry><entry>146-162 (138-170)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.90</entry><entry>Transmembrane</entry><entry>  13-29 (9-32)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −9.50</entry><entry>Transmembrane</entry><entry>108-124 (104-129)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.75</entry><entry>Transmembrane</entry><entry>  40-56 (33-61)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.64</entry><entry>Transmembrane</entry><entry>177-193 (170-195)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.35</entry><entry>Transmembrane</entry><entry>  77-93 (77-97)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6243(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8517&gt; which encodes amino acid sequence &lt;SEQ ID 8518&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 206

A DNA sequence (GBSx0220) was identified in <i>S. agalactiae </i>&lt;SEQ ID 661&gt; which encodes the amino acid sequence &lt;SEQ ID 662&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00658" num="00658"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2374(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00659" num="00659"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB89623 GB: AE000990 repressor protein [<i>Archaeoglobus</i></entry><entry /></row><row><entry><i>fulgidus</i>]</entry></row><row><entry>Identities = 34/62 (54%), Positives = 46/62 (73%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>LKQVREDIGMTQQELAIRIGVRRETIGHLENNRYNPSLEMALKIVKIFDMKIEDIFQLRK</entry><entry>70</entry><entry /></row><row><entry /><entry /><entry>+K+ R    MTQ+ELA R+GVRRETI  LE  +YNPSL++A KI ++F+ KIEDIF   +</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>IKEFRAKFNMTQEELAKRVGVRRETIVFLEKGKYNPSLKLAYKIARVFNAKIEDIFIFDE</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>71</entry><entry>ED</entry><entry>72</entry></row><row><entry /><entry /><entry>E+</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>EE</entry><entry>66</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 412.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 207

A DNA sequence (GBSx0221) was identified in <i>S. agalactiae </i>&lt;SEQ ID 663&gt; which encodes the amino acid sequence &lt;SEQ ID 664&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00660" num="00660"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3794 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00661" num="00661"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB61817 GB: AL133236 putative acetyl transferase [<i>Streptomyces</i></entry><entry /></row><row><entry><i>coelicolor </i>A3(2)]</entry></row><row><entry>Identities = 30/97 (30%), Positives = 52/97 (52%), Gaps = 1/97 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>82</entry><entry>VGMLNIVTLARADMQWGELGYVFHNQFWSNGYAFESILALLNSTYEKLGFHHIEAQITPG</entry><entry>141</entry><entry /></row><row><entry /><entry /><entry>VGM ++   +    Q GE+ Y+ H + W  G   E   +LL+  +++ G H I A   P</entry></row><row><entry>Sbjct:</entry><entry>72</entry><entry>VGMGDLHVRSHTQRQ-GEISYIVHPRVWGQGIGTEIGRSLLSLGFDRWGLHRIRATCDPR</entry><entry>130</entry></row><row><entry /></row><row><entry>Query:</entry><entry>142</entry><entry>NERSEKLVRRLGLTYETTRKDFSFENGKWTDKLIYSI</entry><entry>178</entry></row><row><entry /><entry /><entry>N+ S +++ +LG+TYE   +  ++    W D L++SI</entry></row><row><entry>Sbjct:</entry><entry>131</entry><entry>NQASSRVLTKLGMTYEGRHRHTAWIRDGWRDSLVFSI</entry><entry>167</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 208

A DNA sequence (GBSx0222) was identified in <i>S. agalactiae </i>&lt;SEQ ID 665&gt; which encodes the amino acid sequence &lt;SEQ ID 666&gt;. This protein is predicted to be p20 protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00662" num="00662"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1044 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00663" num="00663"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA30415 GB: X07542 P20 (AA 1-178) [<i>Bacillus licheniformis</i>]</entry><entry /></row><row><entry>Identities = 56/175 (32%), Positives = 94/175 (53%), Gaps = 6/175 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>16</entry><entry>TVLTERLRLQPVELTNVNDFLEFSSDSETVFYMQRYKANTVEEAQVVLA---NVCMKSPL</entry><entry>72</entry><entry /></row><row><entry /><entry /><entry>T+ TERL L+ +EL + +   ++ SD E   YM       V +A+ ++    ++ ++</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>TLYTERLTLRKMELEDADVLCQYWSDPEVTKYMNITPFTDVSQARDMIQMINDLSLEGQA</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>73</entry><entry>GIYAMIEKESQKMIGIIELEIRDEFS--AEFGYILNKNYNGKGYMTEACSKLMSIGFEHL</entry><entry>130</entry></row><row><entry /><entry /><entry>  +++I KE+ ++IG     + D+ +  AE GY L +N+ GKG+ +EA  KL+  GF  L</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>NRFSIIVKETDEVIGTCGFNMIDQENGRAEIGYDLGRNHWGKGFASEAVQKLIDYGFTSL</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>131</entry><entry>DLERIYARFDINNKKSGNVMERIGMKKEGELRHLAKNPKGEWKTRAYYSILKEEY</entry><entry>185</entry></row><row><entry /><entry /><entry>+L RI A+ +  N  S  ++  +  +KEG LR   K  KG       +S+LK EY</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>NLNRIEAKVEPENTPSIKLLNSLSFQKEGLLRDYEK-AKGRLIDVYMFSLLKREY</entry><entry>176</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 209

A DNA sequence (GBSx0223) was identified in <i>S. agalactiae </i>&lt;SEQ ID 669&gt; which encodes the amino acid sequence &lt;SEQ ID 670&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00664" num="00664"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5180 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00665" num="00665"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA87001 GB: Z46902 unknown [<i>Saccharomyces cerevisiae</i>]</entry><entry /></row><row><entry>Identities = 105/224 (46%), Positives = 148/224 (65%), Gaps = 3/224 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MGDVVENFTEGKNPKIDTLNGKTVRIEKINPD-HFEDLFQVYGELSTEDSLTYISFSKFN</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>+G  VE +T    P+   L G T R+E ++ + H  +LF  Y E   +   TY+    F</entry></row><row><entry>Sbjct:</entry><entry>11</entry><entry>VGADVEGWTTRAFPEKVVLKGNTCRLEPLDRERHGSELFSAYSEAG-QKLWTYLPAGPFT</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>SKNEFDVFFQTLLKSEDPYYLAIVDNNTGKVLGTFSLMRIDTKNRVVEMGWVVYSSKLKQ</entry><entry>119</entry></row><row><entry /><entry /><entry>+  E+  F + L +++D    AI++  T + +GT  L+RID  N  +E+G+VV+S +L++</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>NLEEYLEFIKELNETKDTVPFAIINKETERAVGTLCLIRIDEANGSLEVGYVVFSPELQK</entry><entry>129</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>TRIATEAQYLVMKYVFEELCYRRYEWKCDSLNAPSNNSAKRLGFTFEGTFRQAVVYKGRN</entry><entry>179</entry></row><row><entry /><entry /><entry>T IATEAQ+L+MKYVF++L YRRYEWKCDSLN PS  +A RLGF +EGTFRQ VVYKGR</entry></row><row><entry>Sbjct:</entry><entry>130</entry><entry>TIIATEAQFLLMKYVFDDLQYRRYEWKCDSLNGPSRRAAMRLGFKYEGTFRQVVVYKGRT</entry><entry>189</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>RDTNWYSILDKEWPEKKTRFEKWLDDSNFAVNGYQIRSLSSIEQ</entry><entry>223</entry></row><row><entry /><entry /><entry>RDT W+SI+DKEW   +  FE+WLD +NF  NG Q R +++I +</entry></row><row><entry>Sbjct:</entry><entry>190</entry><entry>RDTQWFSIIDKEWLRIRKTFEEWLDKTNFE-NGKQKRGIAAIRE</entry><entry>232</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 210

A DNA sequence (GBSx0224) was identified in <i>S. agalactiae </i>&lt;SEQ ID 671&gt; which encodes the amino acid sequence &lt;SEQ ID 672&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00666" num="00666"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −12.15</entry><entry>Transmembrane</entry><entry>25-41 (20-49)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5861 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

A related GBS gene &lt;SEQ ID 8519&gt; and protein &lt;SEQ ID 8520&gt; were also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00667" num="00667"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 10</entry><entry /></row><row><entry>McG: Discrim Score: −3.31</entry></row><row><entry>GvH: Signal Score (−7.5): −4.44</entry></row><row><entry>Possible site: 39</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="35pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="126pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>ALOM program</entry><entry>count: 1</entry><entry>value: −12.15</entry><entry>threshold: 0.0</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −12.15</entry><entry>Transmembrane</entry><entry>25-41 (20-49)</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="147pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>PERIPHERAL</entry><entry>Likelihood = 11.94</entry><entry>59</entry><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.93</entry><entry /></row><row><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.5861 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

SEQ ID 672 (GBS43) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 5</figref> (lane 4; MW 34 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 13</figref> (lane 9; MW 58 kDa) and in <figref idrefs="DRAWINGS">FIG. 15</figref> (lane 4; MW 59 kDa).

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 211

A DNA sequence (GBSx0225) was identified in <i>S. agalactiae </i>&lt;SEQ ID 673&gt; which encodes the amino acid sequence &lt;SEQ ID 674&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00668" num="00668"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9519&gt; which encodes amino acid sequence &lt;SEQ ID 9520&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 212

A DNA sequence (GBSx0226) was identified in <i>S. agalactiae </i>&lt;SEQ ID 675&gt; which encodes the amino acid sequence &lt;SEQ ID 676&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00669" num="00669"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="77pt" align="center" /><colspec colname="5" colwidth="28pt" align="left" /><colspec colname="6" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −1.54</entry><entry>Transmembrane</entry><entry>165-181 (164-181)</entry><entry /><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −0.85</entry><entry>Transmembrane</entry><entry>67-83 (67-84)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="371pt" align="left" /><colspec colname="2" colwidth="70pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1617 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00670" num="00670"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAA82211 GB: Z28353 similar to a <i>B. subtilis </i>gene (GB:</entry><entry /></row><row><entry>BACHEMEHY_5) [<i>Clostridium pasteurianum</i>]</entry></row><row><entry>Identities = 40/185 (21%), Positives = 87/185 (46%), Gaps = 6/185 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>18</entry><entry>MPKGKQKVILSAIELFASQGFHGTSTAQLAKNAEVSQATIYKYFETKDKLLVFILELIVQ</entry><entry>77</entry><entry /></row><row><entry /><entry /><entry>M K K  +  SAI++F++ G++G +  ++A NA V++ T+Y +F++K+++  +I+E  V</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNKTKDNIFYSAIKVFSNNGYNGATMDEIASNAGVAKGTLYYHFKSKEEIFKYIIEEGVN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>78</entry><entry>TIGRPFFTELSTFSTKEELIHFFVQDRFKFIEKNNDLIKILMQELLINSETSTIFTKLIN</entry><entry>137</entry></row><row><entry /><entry /><entry> +            T  E +    + +   I KN D  K++  +L            ++</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>LMKNEIDEATDKEKTALEKLKAVCRVQLNLIYKNRDFFKVIASQLWGKELRQLELRDIMR</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>138</entry><entry>STDPNITKIFNCLSEGNSL---NKMEILRAVIGQFITFFIQLY-ILNIKPENLEEELKQI</entry><entry>193</entry></row><row><entry /><entry /><entry>+   +I +      E  S+   N + +  A +G   +  + LY ++N + +N+   ++ +</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NYVVHIEEFVKDAMEAGSIKKGNSLFVAYAFLGTLCS--VSLYEVINAENDNINNTIENL</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>194</entry><entry>EKQIL</entry><entry>198</entry></row><row><entry /><entry /><entry>   IL</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>MNYIL</entry><entry>183</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 213

A DNA sequence (GBSx0227) was identified in <i>S. agalactiae </i>&lt;SEQ ID 677&gt; which encodes the amino acid sequence &lt;SEQ ID 678&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00671" num="00671"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2389(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 214

A DNA sequence (GBSx0228) was identified in <i>S. agalactiae </i>&lt;SEQ ID 679&gt; which encodes the amino acid sequence &lt;SEQ ID 680&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00672" num="00672"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 43</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −13.32</entry><entry>Transmembrane</entry><entry>341-357 (333-361)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.93</entry><entry>Transmembrane</entry><entry>253-269 (238-277)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.77</entry><entry>Transmembrane</entry><entry>172-188 (166-196)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −8.01</entry><entry>Transmembrane</entry><entry>225-241 (215-251)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.01</entry><entry>Transmembrane</entry><entry>  21-37 (18-42)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.66</entry><entry>Transmembrane</entry><entry>285-301 (283-301)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6328(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00673" num="00673"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB42664 GB: AL049819 putative integral membrane protein</entry><entry /></row><row><entry>[<i>Streptomyces coelicolor </i>A3(2)]</entry></row><row><entry>Identities = 60/156 (38%), Positives = 101/156 (64%), Gaps = 1/156 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>176</entry><entry>LMGFMVFFFVFLISGMALLKERTSGTLDRLLATPVKRSDIVFGYMLSYGILAIIQTIVIV</entry><entry>235</entry><entry /></row><row><entry /><entry /><entry>L+G      +FL++ +A L+ERTSGTL+RLLA P+ + D++ GY L++G LAI+Q+ +</entry></row><row><entry>Sbjct:</entry><entry>77</entry><entry>LLGIFPLITMFLVTSIATLRERTSGTLERLLAMPLGKGDLIAGYALAFGALAIVQSALAT</entry><entry>136</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>LSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILMSTLAKSEFQMMQFIPLIIMPQLFF</entry><entry>295</entry></row><row><entry /><entry /><entry>   +W L + V GS + +++V  + AL+  +LG+ +S  A SEFQ +QF+P +I PQL</entry></row><row><entry>Sbjct:</entry><entry>137</entry><entry>GLAVWFLGLDVTGSPWLLLLVALLDALLGTALGLFVSAFAASEFQAVQFMPAVIFPQLLL</entry><entry>196</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>SGII-PLENMASWAQTVGKILPLSYSGDALTKIIMY</entry><entry>330</entry></row><row><entry /><entry /><entry> G+  P +NM    + V  +LP+SY+ D + +++ +</entry></row><row><entry>Sbjct:</entry><entry>197</entry><entry>CGLFTPRDNMHPALEAVSDVLPMSYAVDGMNEVLRH</entry><entry>232</entry></row></tbody></tgroup></table></tables>

There is also homology to a DNA sequence which was identified in <i>S. pyogenes </i>&lt;SEQ ID 681&gt; which encodes the amino acid sequence &lt;SEQ ID 682&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00674" num="00674"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 39</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −11.41</entry><entry>Transmembrane</entry><entry>263-279 (246-284)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.70</entry><entry>Transmembrane</entry><entry>231-247 (224-258)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry>  20-36 (18-39)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.72</entry><entry>Transmembrane</entry><entry>349-365 (345-368)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.45</entry><entry>Transmembrane</entry><entry>187-203 (182-204)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5564(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00675" num="00675"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB12662 GB: Z99108 similar to ABC transporter (ATP-binding</entry><entry /></row><row><entry>protein) [<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 92/369 (24%), Positives = 180/369 (47%),</entry></row><row><entry>Gaps = 25/369 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>12</entry><entry>IKRKKTSYVTFFLMPILTTLLALSLSFSNNNQAKIGILDKDNSQISKQFIAQLKQNKKYD</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>I +K  +Y+  F  P+L T +  S+   N+++ ++ I+D+D++ +S+ +I QLK +</entry></row><row><entry>Sbjct:</entry><entry>15</entry><entry>IFKKPQNYLIMFAAPLLLTFVFGSMLSGNDDKVRLAIVDQDDTILSQHYIRQLKAHDDMY</entry><entry>74</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>IFTKIKKEHIDHYLQDKSLEAVLTIDKGFSDKVLQGKSQKLNIRSIANSEITEWVKAQTN</entry><entry>131</entry></row><row><entry /><entry /><entry>+F  + +      L+ K +  ++ I + F  ++ +GK  +L  R          VK</entry></row><row><entry>Sbjct:</entry><entry>75</entry><entry>VFENMSESKASEKLKQKKIAGIIVISRSFQTQLEKGKHPELIFRHGPELSEAPMVKQYAE</entry><entry>134</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>YLLENYNIIGDVALGNEDTFNR---------ILQKNQQLNYDVKQVTLTDRSRSKAVSST</entry><entry>182</entry></row><row><entry /><entry /><entry>  L   NI    A     T              +K++ +   V + TL+D+      S T</entry></row><row><entry>Sbjct:</entry><entry>135</entry><entry>SALATLNIQVTAAKTASQTAGENWKAAYKTVFAKKHEDIVPAVTRQTLSDKKEGAEASDT</entry><entry>194</entry></row><row><entry /></row><row><entry>Query:</entry><entry>183</entry><entry>TT---GFLLILMLGSTSVIYSGILADKSSQLYHRLMLSNLSRFR----YMLSYVCVGFVA</entry><entry>235</entry></row><row><entry /><entry /><entry> +   GF ++ ++ +       IL  + + ++ RL+ +++SR      Y+LS+  +G++</entry></row><row><entry>Sbjct:</entry><entry>195</entry><entry>ASRAAGFSILFVMLTMMGAAGTILEARKNGVWSRLLTASVSRAEIGAGYVLSFFVIGWIQ</entry><entry>254</entry></row><row><entry /></row><row><entry>Query:</entry><entry>236</entry><entry>FTIQIVIMLSLLKVFNISFFVPTSLLLIIFFLFSLLAIGFGLLIGAITQNSQQSSQLANL</entry><entry>295</entry></row><row><entry /><entry /><entry>F I   ++LS   +F I++  P ++++++  LF L  +G GL+I A  +  +Q     NL</entry></row><row><entry>Sbjct:</entry><entry>255</entry><entry>FGI---LLLSTHWLFGINWGNPAAVIVLVS-LFLLTVVGIGLMIAANVRTPEQQLAFGNL</entry><entry>310</entry></row><row><entry /></row><row><entry>Query:</entry><entry>296</entry><entry>IVMPTSMLAGCLWPLSITPSYMQAIGKLLPQNWVLSAIA-IFQSGGTLSQAWPYLLALMG</entry><entry>354</entry></row><row><entry /><entry /><entry> V+ T M++G  WP+ I P +MQ+I + LPQ W +S +  I  +G  ++     +L + G</entry></row><row><entry>Sbjct:</entry><entry>311</entry><entry>FVIATCMVSGMYWPIDIEPKFMQSIAEFLPQKWAMSGLTEIIANGARVTD----ILGICG</entry><entry>366</entry></row><row><entry /></row><row><entry>Query:</entry><entry>355</entry><entry>TALALISFS</entry><entry>363</entry></row><row><entry /><entry /><entry>  LA  + +</entry></row><row><entry>Sbjct:</entry><entry>367</entry><entry>ILLAFAAIT</entry><entry>375</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00676" num="00676"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 92/375 (24%), Positives = 164/375 (43%),</entry><entry /></row><row><entry>Gaps = 66/375 (17%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>IKELF----RDKRTLAMMFLAPILIMFLMNVMFSANSNTKVKIGTINVNTKVVSNLDNIK</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>IK LF    R K +    FL PIL   L+ +  S ++N + KIG ++ +   +S</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>IKTLFVKIKRKKTSYVTFFLMPILTT-LLALSLSFSNNNQAKIGILDKDNSQISK-----</entry><entry>58</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>HIQVRSFKFNSSAKKALKSNKIDALISEDNKSYTVFYANTDSSKTTLT-RQAFKTAVNTM</entry><entry>125</entry></row><row><entry /><entry /><entry>       +F +     LK NK   + ++  K +   Y    S +  LT  + F   V</entry></row><row><entry>Sbjct:</entry><entry>59</entry><entry>-------QFIAQ----LKQNKKYDIFTKIKKEHIDHYLQDKSLEAVLTIDKGFSDKVLQG</entry><entry>107</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>NSKELISQVKILANKNPKLAQSLQTRSKYIKEKYNY------GNKNT-----------GF</entry><entry>168</entry></row><row><entry /><entry /><entry> S++L     I +  N ++ + ++ ++ Y+ E YN       GN++T           +</entry></row><row><entry>Sbjct:</entry><entry>108</entry><entry>KSQKL----NIRSIANSEITEWVKAQTNYLLENYNIIGDVALGNEDTFNRILQKNQQLNY</entry><entry>163</entry></row><row><entry /></row><row><entry>Query:</entry><entry>169</entry><entry>FAKMIPIL------------MGFMVFFFVFLISGM--ALLKERTSGTLDRLLATPVKRSD</entry><entry>214</entry></row><row><entry /><entry /><entry>  K + +              GF++   +   S +   +L +++S    RL+ + + R</entry></row><row><entry>Sbjct:</entry><entry>164</entry><entry>DVKQVTLTDRSRSKAVSSTTTGFLLILMLGSTSVIYSGILADKSSQLYHRLMLSNLSR--</entry><entry>221</entry></row><row><entry /></row><row><entry>Query:</entry><entry>215</entry><entry>IVFGYMLSY---GILAIIQTIVIVLSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILM</entry><entry>271</entry></row><row><entry /><entry /><entry>  F YMLSY   G +A    IVI+LS + + +I        ++I+ F+ +L+A+ G+L+</entry></row><row><entry>Sbjct:</entry><entry>222</entry><entry>--FRYMLSYVCVGFVAFTIQIVIMLSLLKVFNISFFVPTSLLLIIFFLFSLLAIGFGLLI</entry><entry>279</entry></row><row><entry /></row><row><entry>Query:</entry><entry>272</entry><entry>STLAKSEFQMMQFIPLIIMPQLFFSGII-PLENMASWAQTVGKILPLSYSGDALTKIIMY</entry><entry>330</entry></row><row><entry /><entry /><entry>  + ++  Q  Q   LI+MP    +G + PL    S+ Q +GK+LP ++   A+  I</entry></row><row><entry>Sbjct:</entry><entry>280</entry><entry>GAITQNSQQSSQLANLIVMPTSMLAGCLWPLSITPSYMQAIGKLLPQNWVLSAIA-IFQS</entry><entry>338</entry></row><row><entry /></row><row><entry>Query:</entry><entry>331</entry><entry>GQGLPNVSSNLLVLL</entry><entry>345</entry></row><row><entry /><entry /><entry>G  L      LL L+</entry></row><row><entry>Sbjct:</entry><entry>339</entry><entry>GGTLSQAWPYLLALM</entry><entry>353</entry></row></tbody></tgroup></table></tables>

A further related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 9081&gt; which encodes the amino acid sequence &lt;SEQ ID 9082&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00677" num="00677"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.52</entry><entry>Transmembrane</entry><entry>  21-37 (17-43)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.30</entry><entry>Transmembrane</entry><entry>351-367 (346-371)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.36</entry><entry>Transmembrane</entry><entry>262-278 (260-285)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.60</entry><entry>Transmembrane</entry><entry>288-304 (288-305)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.81</entry><entry>Transmembrane</entry><entry>229-245 (229-246)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.6010(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS sequences follows:

<tables id="TABLE-US-00678" num="00678"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Score = 62.5 bits (149), Expect = 9e−12</entry><entry /></row><row><entry>Identities = 72/382 (18%), Positives = 166/382 (42%), Gaps = 32/382 (8%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MVLFHLIKKESLQIFRNRTALLMMVIFPILMIVILSFAFKSSFNTATTVPKLTIRYQLEG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M +  + +K   ++FR++  L MM + PIL++ +++  F ++ NT   +  + +  ++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRIIAITEKVIKELFRDKRTLAMMFLAPILIMFLMNVMFSANSNTKVKIGTINVNTKVVS</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EKTDYQKNFLAFLKVLNQKLHLETKPSNSLEKDRQRVSEGALTAVLEVKKNQTIKVITNN</entry><entry>120</entry></row><row><entry /><entry /><entry>               L+   H++ +        ++ +    + A++  + N++  V   N</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>N--------------LDNIKHIQVRSFKFNSSAKKALKSNKIDALIS-EDNKSYTVFYAN</entry><entry>105</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>INQQNADLINMLVKNYVDNAKTYDSIAALY------PQQLNHIRKRSVDYVKVSSIQTSK</entry><entry>174</entry></row><row><entry /><entry /><entry> +     L     K  V+   + + I+ +       P+    ++ RS  Y+K    + +</entry></row><row><entry>Sbjct:</entry><entry>106</entry><entry>TDSSKTTLTRQAFKTAVNTMNSKELISQVKILANKNPKLAQSLQTRS-KYIKE---KYNY</entry><entry>161</entry></row><row><entry /></row><row><entry>Query:</entry><entry>175</entry><entry>GMTSADYYA----ISMFTMITFYSMMSAMNLVLSDRQQRITNRIHLTGVSPSFLVFGKLI</entry><entry>230</entry></row><row><entry /><entry /><entry>G  +  ++A    I M  M+ F+  + +   +L +R     +R+  T V  S +VFG ++</entry></row><row><entry>Sbjct:</entry><entry>162</entry><entry>GNKNTGFFAKMIPILMGFMVFFFVFLISGMALLKERTSGTLDRLLATPVKRSDIVFGYML</entry><entry>221</entry></row><row><entry /></row><row><entry>Query:</entry><entry>231</entry><entry>GAMLATTVQLSLLYIFTRFVLRVNWGTNEWMLIGITASLVYLSVAIGIGLGISIKNEAFL</entry><entry>290</entry></row><row><entry /><entry /><entry>   +   +Q  ++ + T ++L +    + + +I +   L  +++++GI +    K+E  +</entry></row><row><entry>Sbjct:</entry><entry>222</entry><entry>SYGILAIIQTIVIVLSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILMSTLAKSEFQM</entry><entry>281</entry></row><row><entry /></row><row><entry>Query:</entry><entry>291</entry><entry>TVASNTIIPIFAFLGGSYVPLTTLHSSIINQLSNISPIKWVNDSLFYLIFGGQYNP-IPV</entry><entry>349</entry></row><row><entry /><entry /><entry>      II    F  G  +PL  + +S    +  I P+ +  D+L  +I  GQ  P +</entry></row><row><entry>Sbjct:</entry><entry>282</entry><entry>MQFIPLIIMPQLFFSG-IIPLENM-ASWAQTVGKILPLSYSGDALTKIIMYGQGLPNVSS</entry><entry>339</entry></row><row><entry /></row><row><entry>Query:</entry><entry>350</entry><entry>TLIVNISIGTIFIILALIGMRK</entry><entry>371</entry></row><row><entry /><entry /><entry> L+V +    I  I  + G+++</entry></row><row><entry>Sbjct:</entry><entry>340</entry><entry>NLLVLLLFLIILTIANIFGLKR</entry><entry>361</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 215

A DNA sequence (GBSx0229) was identified in <i>S. agalactiae </i>&lt;SEQ ID 683&gt; which encodes the amino acid sequence &lt;SEQ ID 684&gt;. This protein is predicted to be CG1718 gene product (b0794). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00679" num="00679"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.17</entry><entry>Transmembrane</entry><entry>118-134 (117-134)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1468(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8521&gt; which encodes amino acid sequence &lt;SEQ ID 8522&gt; was also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00680" num="00680"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop: Possible site: −1 Crend: 8</entry><entry /></row><row><entry>McG: Discrim Score: −10.96</entry></row><row><entry>GvH: Signal Score (−7.5): −4.84</entry></row><row><entry>     Possible site: 15</entry></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry>ALOM program count: 1 value: −1.17 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −1.17</entry><entry>Transmembrane</entry><entry>142-158 (141-158)</entry><entry /></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 4.98</entry><entry>197</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 0.73</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.1468(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00681" num="00681"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAF50837 GB:AE003568 CG1718 gene product [<i>Drosophila melanogaster</i>]</entry><entry /></row><row><entry>Identities = 80/204 (39%), Positives = 123/204 (60%), Gaps = 3/204 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>EIIGLIGPSGAGKSTLIKTMLGMEKADKGTALV--LDTQMPDRNILNQIGYMAQSDALYE</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>E  GL+G +GAGK+T  K M G E+   G A V  L  +    +I   IGY  Q DAL +</entry></row><row><entry>Sbjct:</entry><entry>1394</entry><entry>ECFGLLGVNGAGKTTTFKMMTGDERISSGAAYVQGLSLESNMNSIYKMIGYCPQFDALLD</entry><entry>1453</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>SLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRLSLAIAL</entry><entry>124</entry></row><row><entry /><entry /><entry> LTG E L  F  ++G+Q++ ++Q    ++K       +DK    YSGG KR+LS AIA+</entry></row><row><entry>Sbjct:</entry><entry>1454</entry><entry>DLTGREVLRIFCMLRGVQESRIRQLSEDLAKSFGFMKHIDKQTHAYSGGNKRKLSTAIAV</entry><entry>1513</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>LGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSKVALLLR</entry><entry>183</entry></row><row><entry /><entry /><entry>+G+P+V+ LDEPT G+DP+ RR++W  +  I+D G SI +T+H M+E E L +++A+++</entry></row><row><entry>Sbjct:</entry><entry>1514</entry><entry>IGSPSVIYLDEPTTGMDPAARRQLWNMVCRIRDSGKSIVLTSHSMEECEALCTRLAIMVN</entry><entry>1573</entry></row><row><entry /></row><row><entry>Query:</entry><entry>184</entry><entry>GNIIAFDTPLHLKKQFNVSTIEEV</entry><entry>207</entry></row><row><entry /><entry /><entry>G      +  HLK +F+   I ++</entry></row><row><entry>Sbjct:</entry><entry>1574</entry><entry>GEFKCIGSTQHLKNKFSKGLILKI</entry><entry>1597</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Identities = 73/216 (33%), Positives = 128/216 (58%), Gaps = 9/216 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEVFKGEIIGLIGPSGAGKSTLIKTMLGMEKADKGTALV--LDTQMPDRNILNQIGYMAQ</entry><entry>58</entry><entry /></row><row><entry /><entry /><entry>M +F+ EI  L+G +GAGK+T I  + GM     GTA++   D +         +G   Q</entry></row><row><entry>Sbjct:</entry><entry>536</entry><entry>MNMFEDEITVLLGHNGAGKTTTISMLTGMFPPTSGTAIINGSDIRTNIEGARMSLGICPQ</entry><entry>595</entry></row><row><entry /></row><row><entry>Query:</entry><entry>59</entry><entry>SDALYESLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRL</entry><entry>118</entry></row><row><entry /><entry /><entry> + L++ ++   ++ FF +MKG++   ++Q++    K+++LE++ +   S  SGGMKR+L</entry></row><row><entry>Sbjct:</entry><entry>596</entry><entry>HNVLFDEMSVSNHIRFFSRMKGLRGKAVEQEVAKYLKMIELEDKANVASSKLSGGMKRKL</entry><entry>655</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>SLAIALLGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSK</entry><entry>177</entry></row><row><entry /><entry /><entry>S+  AL G+  V++ DEP+ G+DPS RR++W +L+  +  G ++ +TTH MDEA+ L  +</entry></row><row><entry>Sbjct:</entry><entry>656</entry><entry>SVCCALCGDTKVVLCDEPSSGMDPSARRQLW-DLLQQEKVGRTLLLTTHFMDEADVLGDR</entry><entry>714</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>VALLLRGNIIAFDTPLHLKKQFN-----VSTIEEVF</entry><entry>208</entry></row><row><entry /><entry /><entry>+A++  G +    T   LKKQ+      VS ++ +F</entry></row><row><entry>Sbjct:</entry><entry>715</entry><entry>IAIMCDGELKCQGTSFFLKKQYGSGYRLVSGVQNLF</entry><entry>750</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 685&gt; which encodes the amino acid sequence &lt;SEQ ID 686&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00682" num="00682"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="56pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.43</entry><entry>Transmembrane</entry><entry>49-65 (49-65)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1171(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00683" num="00683"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB12660 GB:Z99108 similar to ABC transporter (ATP-binding protein)</entry><entry /></row><row><entry>[<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 151/316 (47%), Positives = 202/316 (63%), Gaps = 18/316 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>VQLTNVVKSYKNGKKA-VNDVSLSIEAGNIYGLLGPNGAGKSTLINLILGLIPLSSGKIT</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>+Q  N+ K+Y  GKK  V  +S S++ G  +GLLGPNGAGKST I++I GL+P  SG IT</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>LQAENIKKAY--GKKTIVKGISFSLKKGESFGLLGPNGAGKSTTISMISGLVPHDSGNIT</entry><entry>59</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>VLGQS-QKTIRKISSQIGYVPQDIAVYPDLTAYENVELFGSLYGLKGAQLKKQVLKSLEF</entry><entry>121</entry></row><row><entry /><entry /><entry>V G    K   K   +IG VPQ+IA+YP LTA+EN+  +G +YGL   + KK+  + LE+</entry></row><row><entry>Sbjct:</entry><entry>60</entry><entry>VGGYVIGKETAKAKQKIGIVPQEIALYPTLTAHENLMFWGKMYGLTHDEAKKRAAEVLEY</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>VGLHSQAKQFPSQFSGGMKRRLNIACALVHSPKLIIFDEPTVGIDPQSRNHILESIRLLN</entry><entry>181</entry></row><row><entry /><entry /><entry>VGL  +AK     FSGGMKRR+NI  AL+H P+L+I DEPTVGIDPQSRNHILE+++ LN</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>VGLTERAKDKIETFSGGMKRRINIGAALMHKPELLIMDEPTVGIDPQSRNHILETVKQLN</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>KEGATVIYTTHYMEEVEALCDYIFIMDHGQVIEEGPKFELEKRYVANLANQIIVTLTDSR</entry><entry>241</entry></row><row><entry /><entry /><entry>+ G TVIYT+HYMEEVE LCD I I+D G++I  G K +L  R   +   Q+ V+  +</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>ETGMTVIYTSHYMEEVEFLCDRIGIIDQGEMIAIGTKTDLCSRLGGDTIIQLTVSGINEA</entry><entry>239</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>HL----ELADKPDWSLIEDGEKLMLKIDNSD------MTSVVHQLTQANITFSEIRHNHL</entry><entry>291</entry></row><row><entry /><entry /><entry> L     LA   D ++ E    L LKID S       +TS++ + T  +I    ++</entry></row><row><entry>Sbjct:</entry><entry>240</entry><entry>FLVAIRSLAHVNDVTVHE----LELKIDISAAHHEKVVTSLLAEATAHHINLLSLQVQEP</entry><entry>295</entry></row><row><entry /></row><row><entry>Query:</entry><entry>292</entry><entry>NLEEIFLHLTGKKLRD</entry><entry>307</entry></row><row><entry /><entry /><entry>NLE +FL+LTG+ LRD</entry></row><row><entry>Sbjct:</entry><entry>296</entry><entry>NLERLFLNLTGRTLRD</entry><entry>311</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00684" num="00684"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 81/211 (38%), Positives = 125/211 (58%), Gaps = 2/211 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MEVFKGEIIGLIGPSGAGKSTLIKTMLGMEKADKGTALVL-DTQMPDRNILNQIGYMAQS</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>+ +  G I GL+GP+GAGKSTLI  +LG+     G   VL  +Q   R I +QIGY+ Q</entry></row><row><entry>Sbjct:</entry><entry>25</entry><entry>LSIEAGNIYGLLGPNGAGKSTLINLILGLIPLSSGKITVLGQSQKTIRKISSQIGYVPQD</entry><entry>84</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>DALYESLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRLS</entry><entry>119</entry></row><row><entry /><entry /><entry> A+Y  LT  EN+  FG + G++  +LK+Q+    + V L +Q  +F S +SGGMKRRL+</entry></row><row><entry>Sbjct:</entry><entry>85</entry><entry>IAVYPDLTAYENVELFGSLYGLKGAQLKKQVLKSLEFVGLHSQAKQFPSQFSGGMKRRLN</entry><entry>144</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>LAIALLGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSKV</entry><entry>178</entry></row><row><entry /><entry /><entry>+A AL+ +P ++I DEPTVGIDP  R  I + +  +  EG ++  TTH M+E E L   +</entry></row><row><entry>Sbjct:</entry><entry>145</entry><entry>IACALVHSPKLIIFDEPTVGIDPQSRNHILESIRLLNKEGATVIYTTHYMEEVEALCDYI</entry><entry>204</entry></row><row><entry /></row><row><entry>Query:</entry><entry>179</entry><entry>ALLLRGNIIAFDTPLHLKKQFNVSTIEEVFL</entry><entry>209</entry></row><row><entry /><entry /><entry> ++  G +I       L+K++  +   ++ +</entry></row><row><entry>Sbjct:</entry><entry>205</entry><entry>FIMDHGQVIEEGPKFELEKRYVANLANQIIV</entry><entry>235</entry></row></tbody></tgroup></table></tables>

SEQ ID 8522 (GBS391) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 74</figref> (lane 7; MW 30 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 83</figref> (lane 4; MW 55 kDa).

GBS391-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 217</figref>, lane 3.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 216

A DNA sequence (GBSx0230) was identified in <i>S. agalactiae </i>&lt;SEQ ID 687&gt; which encodes the amino acid sequence &lt;SEQ ID 688&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00685" num="00685"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.6732(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 217

A repeated DNA sequence (GBSx0231) was identified in <i>S. agalactiae </i>&lt;SEQ ID 689&gt; which encodes the amino acid sequence &lt;SEQ ID 690&gt;. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00686" num="00686"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00687" num="00687"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAC18596 GB:AJ278419 IS1381 transposase [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 111/129 (86%), Positives = 117/129 (90%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKAQAIVTSQGRIVSLDIAVNYCHDMKLFKMSRRNIGQAAKILADSGYQGIMKMYSQAQT</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MK QAIVTSQGRIVSLDI VNYCHDMKLFKMSRRNIGQA KILADSGYQG+MK+Y QAQT</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MKTQAIVTSQGRIVSLDITVNYCHDMKLFKMSRRNIGQAGKILADSGYQGLMKIYPQAQT</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>PRKSSKLKPLTLEDKTYNHTLSKERIKVENIFAKVKTFKIFSTTYRNRRKRFGLRMNLIA</entry><entry>120</entry></row><row><entry /><entry /><entry> RKSSKLKPLT+EDK  NH LSKER KVENIFAKVKTFK+FSTTYR+ RKRFGLRMNL A</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>SRKSSKLKPLTVEDKACNHALSKERSKVENIFAKVKTFKMFSTTYRSHRKRFGLRMNLSA</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GMINRELGF</entry><entry>129</entry></row><row><entry /><entry /><entry>G+IN ELGF</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GIINHELGF</entry><entry>129</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 218

A repeated DNA sequence (GBSx0232) was identified in <i>S. agalactiae </i>&lt;SEQ ID 691&gt; which encodes the amino acid sequence &lt;SEQ ID 692&gt;. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00688" num="00688"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3996(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00689" num="00689"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAC18595 GB:AJ278419 IS1381 transposase [<i>Streptococcus pneumoniae</i>]</entry><entry /></row><row><entry>Identities = 110/125 (88%), Positives = 119/125 (95%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MNYEASKQLTDVRFKRLVGVQRTTFEEMLAVLKTAYQRKHAKGGRTPKLSLEDLLMATLQ</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MNYEASKQLTD RFKRLVGVQRTTFEEMLAVLKTAYQ KHAKGGR PKLSLEDLLMATLQ</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MNYEASKQLTDARFKRLVGVQRTTFEEMLAVLKTAYQLKHAKGGRKPKLSLEDLLMATLQ</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>YMREYRTYEQIAADFGIHESNLIRRSQWVESTLIQSGFTISKTHLSAEDTVIVDATEVKI</entry><entry>120</entry></row><row><entry /><entry /><entry>Y+REYRTYE+IAADFG+HESNL+RRSQWVE TL+QSG TIS+T LS+EDTV++DATEVKI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>YVREYRTYEEIAADFGVHESNLLRRSQWVEVTLVQSGVTISRTPLSSEDTVMIDATEVKI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NRPKK</entry><entry>125</entry></row><row><entry /><entry /><entry>NRPKK</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NRPKK</entry><entry>125</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 219

A DNA sequence (GBSx0233) was identified in <i>S. agalactiae </i>&lt;SEQ ID 693&gt; which encodes the amino acid sequence &lt;SEQ ID 694&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00690" num="00690"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.40</entry><entry>Transmembrane</entry><entry>130-146 (123-156)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −7.86</entry><entry>Transmembrane</entry><entry>169-185 (167-191)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.90</entry><entry>Transmembrane</entry><entry>100-116 (95-118)</entry></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.52</entry><entry>Transmembrane</entry><entry>199-215 (189-216)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5161(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00691" num="00691"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:BAB04126 GB:AP001508 unknown conserved protein in others</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 47/207 (22%), Positives = 95/207 (45%), Gaps = 14/207 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>LQKENTLLEGRIDNSNNQTYTDMIVYLRGA-SISPYHQELIRNDIVNMLLEAQERQASLV</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>L K+N      +   N + Y D+++Y+R A S S    E +  ++++ LLEAQ +  S</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>LIKDNNEKRKLLTEENLKVYEDLLLYIRLAHSKSEQETEELLTELLDHLLEAQAKGKSAK</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>SVFGEDRHDFINQVIKSTPKISKKEE-TLQRWDLAILLLTIQMIIFLGGYLITEALQQSV</entry><entry>124</entry></row><row><entry /><entry /><entry>+VFG++   + +++I   PK+  KE   L  + L++   T+  ++F G Y +       V</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>AVFGDNPKQYADEIIGEIPKMVTKERFGLFAYGLSMFFATV--LVFSGIYRMLRYYVFQV</entry><entry>123</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>PDLIPITLLDVLFAIFISIIAVKIADTIIYATYNFDK----SKEKKYFFRYIFLILSLII</entry><entry>180</entry></row><row><entry /><entry /><entry> + +    +    A+  +I ++ IA   ++  + + +        K F  +I  +  +I</entry></row><row><entry>Sbjct:</entry><entry>124</entry><entry>GEAVSEVYVGT--ALITTIASIVIAWMFVFVVFQYFRWSCFRTINKVFEFFILWLGGMIP</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>AYILIGKYYHLP----FINIPLWIYLI</entry><entry>203</entry></row><row><entry /><entry /><entry>  +     Y  P     I IP+++Y +</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>FALFFALLYFTPNVGRMIEIPVYLYFV</entry><entry>208</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 220

A DNA sequence (GBSx0234) was identified in <i>S. agalactiae </i>&lt;SEQ ID 695&gt; which encodes the amino acid sequence &lt;SEQ ID 696&gt;. This protein is predicted to be minor extracellular protease epr precursor (epr). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00692" num="00692"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.72</entry><entry>Transmembrane</entry><entry>10-26 (5-33)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5288(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 8523&gt; which encodes amino acid sequence &lt;SEQ ID 8524&gt; was also identified. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00693" num="00693"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Lipop Possible site: −1 Crend: 8</entry><entry /></row><row><entry>McG: Discrim Score: 12.11</entry></row><row><entry>GvH: Signal Score (−7.5): −4.02</entry></row><row><entry>     Possible site: 29</entry></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry>ALOM program count: 1 value: −10.72 threshold: 0.0</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="210pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −10.72</entry><entry>Transmembrane</entry><entry>8-24 (5-33)</entry></row><row><entry /><entry>PERIPHERAL</entry><entry>Likelihood = 13.74</entry><entry>219</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>modified ALOM score: 2.64</entry><entry /></row><row><entry>*** Reasoning Step: 3</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5288(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00694" num="00694"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>!GB:Z99123 extracellular serine protease [<i>Bacillus </i>s . . .</entry><entry /></row><row><entry>&gt;GP:CAB15866 GB:Z99123 extracellular serine protease [<i>Bacillus subtilis</i>]</entry></row><row><entry>Identities = 44/150 (29%), Positives = 80/150 (53%), Gaps = 14/150 (9%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>37</entry><entry>QMDTVESSVNHVSDSQLTEAQDMLDKFEKKPSEKLLKDVELALNKLSNSSKKEALQKRFK</entry><entry>96</entry><entry /></row><row><entry /><entry /><entry>++D V+S  N      + +A+D + K EK  +++ +   + A+NKL N + K+ LQKR</entry></row><row><entry>Sbjct:</entry><entry>428</entry><entry>RLDKVQSYRN------VKDAKDKVAKAEKYKTQQTVDTAQTAINKLPNGTDKKNLQKRLD</entry><entry>481</entry></row><row><entry /></row><row><entry>Query:</entry><entry>97</entry><entry>KAKDKYLKDEADKKATKDATDLVEILEQAPSEENVLKAEAAVNKLTVKESKEALQKRIDT</entry><entry>156</entry></row><row><entry /><entry /><entry>+ K +Y+       A+K A D V   E++  + +V  A++A+ KL     K +LQKR++</entry></row><row><entry>Sbjct:</entry><entry>482</entry><entry>QVK-RYI-------ASKQAKDKVAKAEKSKKKTDVDSAQSAIGKLPASSEKTSLQKRLNK</entry><entry>533</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>VKTQYGLIGNQTPSSSVAETTEQGTANPAS</entry><entry>186</entry></row><row><entry /><entry /><entry>VK+       Q+ S++  ++T+   A   S</entry></row><row><entry>Sbjct:</entry><entry>534</entry><entry>VKSTNLKTAQQSVSAAEKKSTDANAAKAQS</entry><entry>563</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 39/124 (31%), Positives = 64/124 (51%), Gaps = 2/124 (1%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>35</entry><entry>TTQMDTVESSVNHVSDSQLTEAQDMLDKFEKKPSEKLLKDVELALNKLSNSSKKEALQKR</entry><entry>94</entry><entry /></row><row><entry /><entry /><entry>+++  +++  +N V  + L  AQ  +   EKK ++      + A+N+L     K ALQKR</entry></row><row><entry>Sbjct:</entry><entry>521</entry><entry>SSEKTSLQKRLNKVKSTNLKTAQQSVSAAEKKSTDANAAKAQSAVNQLQAGKDKTALQKR</entry><entry>580</entry></row><row><entry /></row><row><entry>Query:</entry><entry>95</entry><entry>FKKAKDKYLKDEADKKATKDATDLVEILEQAPSEENVLKAEAAVNKLTVKESKEALQKRI</entry><entry>154</entry></row><row><entry /><entry /><entry>  K K K    EA K  T  A   V+  E+  ++++   A++AVN+L     K  LQKR+</entry></row><row><entry>Sbjct:</entry><entry>581</entry><entry>LDKVKKKVAAAEAKKVETAKAK--VKKAEKDKTKKSKTSAQSAVNQLKASNEKTKLQKRL</entry><entry>638</entry></row><row><entry /></row><row><entry>Query:</entry><entry>155</entry><entry>DTVK</entry><entry>158</entry></row><row><entry /><entry /><entry>+ VK</entry></row><row><entry>Sbjct:</entry><entry>639</entry><entry>NAVK</entry><entry>642</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 697&gt; which encodes the amino acid sequence &lt;SEQ ID 698&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00695" num="00695"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 41</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="210pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −4.99</entry><entry>Transmembrane</entry><entry>24-40 (23-43)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2996(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00696" num="00696"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;CAB15866 GB:Z99123 extracellular serine protease [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 43/130 (33%), Positives = 71/130 (54%), Gaps = 8/130 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>41</entry><entry>GSHPQTQDKVA---KHSKSAASLLKKAVKAVNDADRLATAAAIQEAQKAVDKLAESSKKK</entry><entry>97</entry><entry /></row><row><entry /><entry /><entry>G  P + +K +   + +K  ++ LK A ++V+ A++ +T A   +AQ AV++L     K</entry></row><row><entry>Sbjct:</entry><entry>516</entry><entry>GKLPASSEKTSLQKRLNKVKSTNLKTAQQSVSAAEKKSTDANAAKAQSAVNQLQAGKDKT</entry><entry>575</entry></row><row><entry /></row><row><entry>Query:</entry><entry>98</entry><entry>TLQEQLN-----VAKAKQEQEDAATQAVKAAEETLNQNLKDIAQKAVNDLSNKGKKAALQ</entry><entry>152</entry></row><row><entry /><entry /><entry> LQ++L+     VA A+ ++ + A   VK AE+   +  K  AQ AVN L    +K  LQ</entry></row><row><entry>Sbjct:</entry><entry>576</entry><entry>ALQKRLDKVKKKVAAAEAKKVETAKAKVKKAEKDKTKKSKTSAQSAVNQLKASNEKTKLQ</entry><entry>635</entry></row><row><entry /></row><row><entry>Query:</entry><entry>153</entry><entry>SRLDAILPAK</entry><entry>162</entry></row><row><entry /><entry /><entry> RL+A+ P K</entry></row><row><entry>Sbjct:</entry><entry>636</entry><entry>KRLNAVKPKK</entry><entry>645</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 31/105 (29%), Positives = 53/105 (49%), Gaps = 1/105 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>54</entry><entry>SKSAASLLKKAVKAVNDADRLATAAAIQEAQKAVDKLAESSKKKTLQEQLNVAKAKQEQE</entry><entry>113</entry><entry /></row><row><entry /><entry /><entry>+++  S    A +AV  A++      I +A++ + +L  S  K  L ++L+  ++ +  +</entry></row><row><entry>Sbjct:</entry><entry>380</entry><entry>AQATDSAYAAAEQAVKKAEQTKAQIDINKARELISQLPNSDAKTALHKRLDKVQSYRNVK</entry><entry>439</entry></row><row><entry /></row><row><entry>Query:</entry><entry>114</entry><entry>DAATQAVKAAEETLNQNLKDIAQKAVNDLSNKGKKAALQSRLDAI</entry><entry>158</entry></row><row><entry /><entry /><entry>DA  +  KA E+   Q   D AQ A+N L N   K  LQ RLD +</entry></row><row><entry>Sbjct:</entry><entry>440</entry><entry>DAKDKVAKA-EKYKTQQTVDTAQTAINKLPNGTDKKNLQKRLDQV</entry><entry>483</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00697" num="00697"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 61/233 (26%), Positives = 115/233 (49%), Gaps = 13/233 (5%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>SMKIDKKELLALIASIILLIFASVTFFLFKDHGTTQMDTVESSVNHVSDSQLTEAQDMLD</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>SM   +KE L  + S++ +     +  +F  H  TQ    + S +  + S L +A   ++</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>SMTKSQKEALYWMLSVLTITLIGGSCLIFGSHPQTQDKVAKHSKS--AASLLKKAVKAVN</entry><entry>69</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>KFEKKPSEKLLKDVELALNKLSNSSKKEALQKRFKKAKDKYLKDEADKKATKDATDLVEI</entry><entry>121</entry></row><row><entry /><entry /><entry>  ++  +   +++ + A++KL+ SSKK+ LQ++   AK K  +++A       AT  V+</entry></row><row><entry>Sbjct:</entry><entry>70</entry><entry>DADRLATAAAIQEAQKAVDKLAESSKKKTLQEQLNVAKAKQEQEDA-------ATQAVKA</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>LEQAPSEENVLKAEAAVNKLTVKESKEALQKRIDTVKTQYGLIGNQTPSSSVAETTEQGT</entry><entry>181</entry></row><row><entry /><entry /><entry> E+  ++     A+ AVN L+ K  K ALQ R+D +     +I ++ P  S  E T+</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>AEETLNQNLKDIAQKAVNDLSNKGKKAALQSRLDAILPAKPII-DEFPRQS-GEITDNSY</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>ANPASQDTSSYVNQNVAPTYE-QPQANNTPVTPGVNNTVP-TPGTGTVPATNG</entry><entry>232</entry></row><row><entry /><entry /><entry>  P   D S   + + +PT +   +++ + VTP  ++  P  P T + P+ +G</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>WTPFPGDVSDTYDNSQSPTLDPSSESSASDVTPQPSHPDPIPPQTSSEPSDSG</entry><entry>233</entry></row></tbody></tgroup></table></tables>

SEQ ID 8524 (GBS278) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 52</figref> (lane 6; MW 40 kDa).

The GBS278-His fusion product was purified (<figref idrefs="DRAWINGS">FIG. 206</figref>, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 305</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 221

A DNA sequence (GBSx0235) was identified in <i>S. agalactiae </i>&lt;SEQ ID 699&gt; which encodes the amino acid sequence &lt;SEQ ID 700&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00698" num="00698"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1466 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 222

A DNA sequence (GBSx0236) was identified in <i>S. agalactiae </i>&lt;SEQ ID 701&gt; which encodes the amino acid sequence &lt;SEQ ID 702&gt;. This protein is predicted to be N-acetylglucosamine-6-phosphate deacetylase (nagA). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00699" num="00699"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4607 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9297&gt; which encodes amino acid sequence &lt;SEQ ID 9298&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00700" num="00700"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAG21688 GB:AY007718 N-acetylglucosamine-6-phosphate deacetylase</entry><entry /></row><row><entry>[<i>Lactococcus lactis </i>subsp. <i>cremoris</i>]</entry></row><row><entry>Identities = 113/178 (63%), Positives = 135/178 (75%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>131</entry><entry>GIYFEGPYFTEEYKGAQNPIYMRNPNLEEFAQWQKAAKGLITKIALAPEREGVEEFVSAI</entry><entry>190</entry><entry /></row><row><entry /><entry /><entry>GI+FEGP+FTEE KGAQNP YMR+  + E   WQ+AA G++ KI LAPEREG E+F+</entry><entry /></row><row><entry>Sbjct:</entry><entry>1</entry><entry>GIFFEGPFFTEEKKGAQNPKYMRDAKMWELEDWQEAAHGMLKKIGLAPEREGSEDFIRKA</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>191</entry><entry>TKQGVTVALGHSNGTYKEAKKAVKAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTYAE</entry><entry>250</entry></row><row><entry /><entry /><entry>T+ GV +ALGHSN TYK+A   V+AGASVWVH +NGM G+TH+EPGMVGA+ N PNTYAE</entry><entry /></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TESGVVIALGHSNATYKQAVAGVQAGASVWVHTFNGMSGMTHQEPGMVGAILNTPNTYAE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>251</entry><entry>LICDGHHVDPVACDILMTQKGHNHVALITDCMAAGGAPDGDYMLGELPVVVSNGTARL</entry><entry>308</entry></row><row><entry /><entry /><entry>LICDGHHV P A +I++  KG +HV LITD M A G PDG YMLGE  V V +G A L</entry><entry /></row><row><entry>Sbjct:</entry><entry>121</entry><entry>LICDGHHVRPEAAEIVVKMKGADHVVLITDSMRAAGLPDGPYMLGEYEVEVRDGAAWL</entry><entry>178</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 703&gt; which encodes the amino acid sequence &lt;SEQ ID 704&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00701" num="00701"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 40</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3114 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00702" num="00702"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 227/300 (75%), Positives = 262/300 (86%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>9</entry><entry>MTKYIKADRFFYADHVKENGYLEIKDNHFGKWIENISGQEEILDYSGYQIAPGLVDTHIH</entry><entry>68</entry><entry /></row><row><entry /><entry /><entry>MT Y+KAD F+Y   V+  GYL + D  FG+W E +    +I+DY+GYQIAPGLVDTHIH</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTCYLKADCFYYPTEVRPAGYLSLHDGVFGEWTEIVPADAQIIDYTGYQIAPGLVDTHIH</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>69</entry><entry>GFAGADVMDCDSEGILRMSAGLLSTGVTSFLPTTLTSDTKRLEEASKSVAAVAGKEQGAK</entry><entry>128</entry></row><row><entry /><entry /><entry>G+AGADVMD  ++GI +MS GLL+TGVTSFLPTTLTS  ++LE+ S ++A+VA + +GAK</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>GYAGADVMDNSAQGIHQMSEGLLATGVTSFLPTTLTSTFEQLEKVSGTIASVADQVKGAK</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>129</entry><entry>IQGIYFEGPYFTEEYKGAQNPIYMRNPNLEEFAQWQKAAKGLITKIALAPEREGVEEFVS</entry><entry>188</entry></row><row><entry /><entry /><entry>IQGIYFEGPYFTEEYKGAQNP YM+ P LEEF  WQKAAKGLI KIALAPER+GV+EFVS</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IQGIYFEGPYFTEEYKGAQNPSYMKTPRLEEFDAWQKAAKGLIKKIALAPERDGVKEFVS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>189</entry><entry>AITKQGVTVALGHSNGTYKEAKKAVKAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY</entry><entry>248</entry></row><row><entry /><entry /><entry>A+TKQGVTVALGHSNGTY+EAK+AV+AGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>AVTKQGVTVALGHSNGTYQEAKEAVQAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>249</entry><entry>AELICDGHHVDPVACDILMTQKGHNHVALITDCMAAGGAPDGDYMLGELPVVVSNGTARL</entry><entry>308</entry></row><row><entry /><entry /><entry>AELICDGHHV P+ACDILM QKGH+HVA+ITDCM AGG+PDGDY+LGE  VVV+NGTARL</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>AELICDGHHVSPIACDILMQQKGHDHVAMITDCMRAGGSPDGDYLLGEFSVVVANGTARL</entry><entry>300</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 223

A DNA sequence (GBSx0237) was identified in <i>S. agalactiae </i>&lt;SEQ ID 705&gt; which encodes the amino acid sequence &lt;SEQ ID 706&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00703" num="00703"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3709(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9307&gt; which encodes amino acid sequence &lt;SEQ ID 9308&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00704" num="00704"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAB16112 GB:Z99124 yyaQ [<i>Bacillus subtilis</i>]</entry><entry /></row><row><entry>Identities = 40/110 (36%), Positives = 62/110 (56%), Gaps = 12/110 (10%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>121</entry><entry>IAKTFEDSVDYPFAKHPQYASYRVSG--KWYALLFPLKMGKLENVPAQLSED---EVEVL</entry><entry>175</entry><entry /></row><row><entry /><entry /><entry>+ + +  S DYP+ K+P YAS R +   KWY L+  +       +P +L  D   E+++L</entry></row><row><entry>Sbjct:</entry><entry>11</entry><entry>VKEKYGTSPDYPWEKYPNYASLRHTSNKKWYGLIMNV-------LPEKLGLDGHGEIDIL</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>176</entry><entry>NIKVNPQDMEILLQKEGIYPSYHMSKKTWVSIVLDNTLSDIEIFKLVSDS</entry><entry>225</entry></row><row><entry /><entry /><entry>N+K  P+  + L   E I P YHM K+ W+SIVL+ T  + EI+ L+  S</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>NLKCPPEISDRLRNGENILPGYHMDKEHWISIVLERTDPEGEIYNLIEQS</entry><entry>113</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 707&gt; which encodes the amino acid sequence &lt;SEQ ID 708&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00705" num="00705"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2541(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00706" num="00706"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 114/247 (46%), Positives = 169/247 (68%), Gaps = 1/247 (0%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>MSIESDFFRKKRFIFSSLEEFGFIKSDQEYIYCQTFMDNDFKAIITISLDGKIAGKVIDS</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>MS+ +D+F ++  I   L  +GF K D  Y Y +FM+ +F+A + I   G I  +VID</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSLATDYFSRQTPIVEKLMAYGFEKRDNGYFYNERFMEGEFEAQLRIDEAGNIWDRVIDC</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>ALEEEYLPLRAANYNGSFVGEVRSAYMAILGDISDSCCKDLLFTKDQSNRLAEKIAKTFE</entry><entry>126</entry></row><row><entry /><entry /><entry> LEE+YLPL+ A + G++ G+VR+AY+ +L  +S +C +   F   Q+NRLA+ I K +</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>DLEEDYLPLQQAAWQGTYTGQVRAAYLELLERLSVACFEATPFQSMQANRLAKHITKEWS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>DSVDYPFAKHPQYASYRVSGKWYALLFPLKMGKLENVPAQLSEDEVEVLNIKVNPQDMEI</entry><entry>186</entry></row><row><entry /><entry /><entry>D +DYPF KHP  A+YRV GKWYA++F L   KL+ + P +L     EV+ +KVNP+</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>DPMDYPFEKHPDLATYRVGGKWYAMIFSLLADKLDQIPERLVGQTCEVMTVKVNPKAFPQ</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>187</entry><entry>LLQKEGIYPSYHMSKKTWVSIVLDNTLSDIEIFKLVSDSRKLVSHNKKSN-SEPEFWIIP</entry><entry>245</entry></row><row><entry /><entry /><entry>LLQ+EGIYP+YHMSKK W+SI+LD+ ++D +++ LV+ SR+LV+ N  SN + P++W+IP</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LLQQEGIYPAYHMSKKNWISIILDDKVTDDKLWTLVTQSRQLVNPNGLSNPNGPDYWVIP</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>246</entry><entry>ANPKFYD</entry><entry>252</entry></row><row><entry /><entry /><entry>AN K+YD</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>ANLKYYD</entry><entry>247</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 224

A DNA sequence (GBSx0238) was identified in <i>S. agalactiae </i>&lt;SEQ ID 709&gt; which encodes the amino acid sequence &lt;SEQ ID 710&gt;. This protein is predicted to be transposase for insertion sequence element is 905. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00707" num="00707"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1824(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9601&gt; which encodes amino acid sequence &lt;SEQ ID 9602&gt; was also identified.

A related GBS nucleic acid sequence &lt;SEQ ID 9595&gt; which encodes amino acid sequence &lt;SEQ ID 9596&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00708" num="00708"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="308pt" align="left" /><colspec colname="2" colwidth="133pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAA25167 GB:L20851 transposase [<i>Lactococcus lactis</i>]</entry><entry /></row><row><entry>Identities = 325/391 (83%), Positives = 365/391 (93%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>12</entry><entry>MTQFTTELLNFLAQKQDIDEFFRSSLETAMNDLLQVELSAFLGYEPYDKAGYNTGNSRNG</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>MTQFTTELLNFLAQKQDIDEFFR+SLETAMNDLLQ ELSAFLGYEPYDK GYN+GNSRNG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTQFTTELLNFLAQKQDIDEFFRTSLETAMNDLLQAELSAFLGYEPYDKVGYNSGNSRNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>AYTRRFETKYGVVNLLIPRDRNGEFSPALIPSYGRRDNHLEEMVIKLYRTGVTTREISDI</entry><entry>131</entry></row><row><entry /><entry /><entry>+Y+R+FETKYG V L IPRDRNG FSPAL+P+YGRRD+HLEEMVIKLY+TGVTTREISDI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>SYSRQFETKYGTVQLSIPRDRNGNFSPALLPAYGRRDDHLEEMVIKLYQTGVTTREISDI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>IERMYGHHYSPATVSNISKATQENVASFHERSLEANYTVLYLDGTYLPLRRGTVSKECIH</entry><entry>191</entry></row><row><entry /><entry /><entry>IERMYGHHYSPAT+SNISKATQENVA+FHERSLEANY+VL+LDGTYLPLRRGTVSKECIH</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IERMYGHHYSPATISNISKATQENVATFHERSLEANYSVLFLDGTYLPLRRGTVSKECIH</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>192</entry><entry>IALGVTSYGHKAILGYDIAPNENNASWSDLLERFKGQGVQQVSLVVSDGFNGLDQLIQQA</entry><entry>251</entry></row><row><entry /><entry /><entry>IALG+T  G KA+LGY+IAPNENNASWS LL++ + QG+QQVSLVV+DGF GL+Q+I QA</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>IALGITPEGQKAVLGYEIAPNENNASWSTLLDKLQNQGIQQVSLVVTDGFKGLEQIISQA</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>252</entry><entry>FPMAKQQRCLVHIGRNIASKVKRADRALILEQFKTIYRAINVEEAKQALDSFINEWKPHY</entry><entry>311</entry></row><row><entry /><entry /><entry>+P+AKQQRCL+HI RN+ASKVKRADRA+ILEQFKTIYRA N+E A QAL++FI EWKP Y</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>YPLAKQQRCLIHISRNLASKVKRADRAVILEQFKTIYRAENLEMAVQALENFIAEWKPKY</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>312</entry><entry>KKVIETLESIENLLIFYEFPHQIWGSIYSTNLIESLNKEIKRQTKKKVVFPNEESLERYL</entry><entry>371</entry></row><row><entry /><entry /><entry>+KV+E+LE+ +NLL FY+FP+QIW SIYSTNLIESLNKEIKRQTKKKV+FPNEE+LERYL</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>RKVMESLENTDNLLTFYQFPYQIWHSIYSTNLIESLNKEIKRQTKKKVLFPNEEALERYL</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>372</entry><entry>VTLFSDYNFKQGQRIHKGFGQCTDTLESLFD</entry><entry>402</entry></row><row><entry /><entry /><entry>VTLF DYNFKQ QRIHKGFGQC DTLESLFD</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>VTLFEDYNFKQSQRIHKGFGQCADTLESLFD</entry><entry>391</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 711&gt; which encodes the amino acid sequence &lt;SEQ ID 712&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00709" num="00709"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3054 (Atfirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00710" num="00710"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 111/128 (86%), Positives = 122/128 (94%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>12</entry><entry>MTQFTTELLNFLAQKQDIDEFFRSSLETAMNDLLQVELSAFLGYEPYDKAGYNTGNSRNG</entry><entry>71</entry><entry /></row><row><entry /><entry /><entry>MTQFTTELLNFLAQKQDIDEFFRSSLE AMNDLLQVELSAFLGYEPY+K GYNTGNSRNG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MTQFTTELLNFLAQKQDIDEFFRSSLEIAMNDLLQVELSAFLGYEPYEKEGYNTGNSRNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>72</entry><entry>AYTRRFETKYGVVNLLIPRDRNGEFSPALIPSYGRRDNHLEEMVIKLYRTGVTTREISDI</entry><entry>131</entry></row><row><entry /><entry /><entry> Y+R+FETKYG+VNL+IPRDRNGEFSP L+PSY RR++HLEE+VIKLY+TGVTTREISDI</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>TYSRQFETKYGLVNLIIPRDRNGEFSPVLLPSYARREDHLEEIVIKLYQTGVTTREISDI</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>132</entry><entry>IERMYGHH</entry><entry>139</entry></row><row><entry /><entry /><entry>I+RMYG H</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>IKRMYGDH</entry><entry>128</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 225

A DNA sequence (GBSx0239) was identified in <i>S. agalactiae </i>&lt;SEQ ID 713&gt; which encodes the amino acid sequence &lt;SEQ ID 714&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00711" num="00711"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 32</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="center" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −12.42</entry><entry>Transmembrane</entry><entry>268-284 (260-286)</entry><entry /></row><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −6.32</entry><entry>Transmembrane</entry><entry>232-248 (231-254)</entry></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.5967 (Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00712" num="00712"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAD40365 GB:AF036485 hypothetical protein [Piasmid pNZ4000]</entry><entry /></row><row><entry>Identities = 69/283 (24%), Positives = 133/283 (46%), Gaps = 9/283 (3%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>11</entry><entry>INVDDLSLQEERF-LPSELLAYARDENESS-FVRDIEGHLALVYQLLDTQGHVDDVRHVP</entry><entry>68</entry><entry /></row><row><entry /><entry /><entry>IN ++ +  E+++ +  +++ Y  D +ES+ +V DI     L   L       D +R++</entry></row><row><entry>Sbjct:</entry><entry>19</entry><entry>INAEERATLEDQYGIDEDIIEYVTDNDESTNYVYDINEDDQLFIFLAPYALDKDALRYIT</entry><entry>78</entry></row><row><entry /></row><row><entry>Query:</entry><entry>69</entry><entry>RVIPVTLFLKEDGLFVLANHKNINLVKKALNRV---EKVDSPKHLLLSLVTAFSKQYFDV</entry><entry>125</entry></row><row><entry /><entry /><entry>+  P  + L +  LF   N   I  V  AL       +V S    +L  +      +  +</entry></row><row><entry>Sbjct:</entry><entry>79</entry><entry>Q--PFGMLLHKGVLFTF-NQSGIPEVNTALYSALDNPEVKSVDAFILETLFTVVVSFIPI</entry><entry>135</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>LDTISEERDKLINDLRKRPNKSNLARLANLQSGTVHLMMGTKQNFEMLTDLQNIEQDKEN</entry><entry>185</entry></row><row><entry /><entry /><entry>   I+++R+ L   L ++   S+L  L+ LQ     L    + N   L  L</entry></row><row><entry>Sbjct:</entry><entry>136</entry><entry>SRAITKKRNYLDKMLNRKTKNSDLVSLSYLQQTLTFLSSAVQTNLSELDRLPKTHFGVGA</entry><entry>195</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>TRNEKMQLQDAIIEARQLSNMCSLNSQVFQELS-SYNNVLSNNLNDNVTTLTIISIGISI</entry><entry>244</entry></row><row><entry /><entry /><entry> +++    +D  IE  Q+  M  + +QV   +  + N++ +NNLND +  LTI S+ +++</entry></row><row><entry>Sbjct:</entry><entry>196</entry><entry>DQDKIDLFEDVQIEGEQVQRMFEIETQVVDRIDHTLNSLANNNLNDTMKFLTIWSLTMAV</entry><entry>255</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>IAMVTSFYGMNVKLPFDSVDAVWVLIILITTIITIMLSIVMYI</entry><entry>287</entry></row><row><entry /><entry /><entry>  +++ FYGMNVKLP   +   W+L + I+ ++ + + I++ +</entry></row><row><entry>Sbjct:</entry><entry>256</entry><entry>PTIISGFYGMNVKLPLAGMQYAWMLTLGISVVLIVAMLIMLKV</entry><entry>298</entry></row></tbody></tgroup></table></tables>

SEQ ID 714 (GBS422) was expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 172</figref> (lane 7; MW 60 kDa).

GBS422-GST was purified as shown in <figref idrefs="DRAWINGS">FIG. 219</figref>, lane 12.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 226

A DNA sequence (GBSx0240) was identified in <i>S. agalactiae </i>&lt;SEQ ID 717&gt; which encodes the amino acid sequence &lt;SEQ ID 718&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00713" num="00713"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 45</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0783(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00714" num="00714"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: CAB61731 GB: AL133220 putative oxidoreductase. [<i>Streptomyces</i></entry><entry /></row><row><entry><i>coelicolor </i>A3(2)]</entry></row><row><entry>Identities = 100/306 (32%), Positives = 152/306 (48%), Gaps = 3/306 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KVRYGVVSTAKVAPRFIEGVRLAGNGEVVAVSSRTLESAQAFANKYHLPKAYDKLEDMLA</entry><entry>62</entry><entry /></row><row><entry /><entry /><entry>KVR+G+++T  +A RF   +    + EVVAV+SRT  SA+ FA ++ +P+AY   E +</entry></row><row><entry>Sbjct:</entry><entry>8</entry><entry>KVRWGILATGGMAARFTADLVDLPDAEVVAVASRTEASAKTFAERFGIPRAYGGWETLAR</entry><entry>67</entry></row><row><entry /></row><row><entry>Query:</entry><entry>63</entry><entry>DESIDVIYVATINQDHYKVAKAALLAGKHVLVEKPFTLTYDQANELFALAESCNLFLMEA</entry><entry>122</entry></row><row><entry /><entry /><entry>DE +DV+YVAT +  H   A   L AG++VL EKPFTL   +A EL ALA    +FLMEA</entry></row><row><entry>Sbjct:</entry><entry>68</entry><entry>DEDVDVVYVATPHSAHRTAAGLCLEAGRNVLCEKPFTLNAREAAELVALARENGVFLMEA</entry><entry>127</entry></row><row><entry /></row><row><entry>Query:</entry><entry>123</entry><entry>QKSVFIPMTQVIKKLLASGEIGEVISISSTTAYPN-IDHVTWFRELELGGGTVHFMAPYA</entry><entry>181</entry></row><row><entry /><entry /><entry>      P+ + +K+L+A G IGEV S+ +              R+   GGG +  +  Y</entry></row><row><entry>Sbjct:</entry><entry>128</entry><entry>MWMYCNPLVRRLKELVADGAIGEVRSLQADFGLAGPFPAAHRLRDPAQGGGALLDLGVYP</entry><entry>187</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>LSYLQYLFDATITHASGTATFPKGQSDSQSKLLLQLSNGVLVDIFLTTRLNLPHEMIIYG</entry><entry>241</entry></row><row><entry /><entry /><entry>+S+ Q L     T  +  A   +   D Q+  LL   N  L  I  +     P+   I G</entry></row><row><entry>Sbjct:</entry><entry>188</entry><entry>VSFAQLLLGEP-TDVAARAVLSEEGVDLQTGALLSYGNDALASIHCSITGGTPNSASITG</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>TEGRLIIPH-FWKTTHAKLVRNDTSARTIQVDMVSDFEKEAYHVSQMILEGQRVSHIMTP</entry><entry>300</entry></row><row><entry /><entry /><entry>+EGR+ +P+ F+   H  L R     +  + D      +   H ++ ++   R     +P</entry></row><row><entry>Sbjct:</entry><entry>247</entry><entry>SEGRIDVPNGFFFPDHFVLHRTGRDPQEFRADPADGPRESLRHEAEEVMRALRAGETESP</entry><entry>306</entry></row><row><entry /></row><row><entry>Query:</entry><entry>301</entry><entry>QLTLSG</entry><entry>306</entry></row><row><entry /><entry /><entry> + L G</entry></row><row><entry>Sbjct:</entry><entry>307</entry><entry>LVPLDG</entry><entry>312</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 227

A DNA sequence (GBSx0241) was identified in <i>S. agalactiae </i>&lt;SEQ ID 721&gt; which encodes the amino acid sequence &lt;SEQ ID 722&gt;. This protein is predicted to be valyl-tRNA synthetase (valS). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00715" num="00715"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 36</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="91pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.00</entry><entry>Transmembrane</entry><entry>794-810 (794-810)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1001(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>             bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00716" num="00716"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAA57558 GB: L08854 valyl-tRNA synthetase [<i>Lactobacillus casei</i>]</entry><entry /></row><row><entry>Identities = 543/881 (61%), Positives = 679/881 (76%), Gaps 12/881 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>LSPKYNPAEVEEGRYQTWLDQDVFKPSGDTEAKPYSIVIPPPNVTGKLHLGHAWDTTLQD</entry><entry>64</entry><entry /></row><row><entry /><entry /><entry>L+PKY+   VEEGRYQ WLD+DVFKPSGD +AKPYSIVIPPPNVTGKLH+GHAWDTTLQD</entry></row><row><entry>Sbjct:</entry><entry>27</entry><entry>LAPKYDHKAVEEGRYQEWLDEDVFKPSGDKKAKPYSIVIPPPNVTGKLHMGHAWDTTLQD</entry><entry>86</entry></row><row><entry /></row><row><entry>Query:</entry><entry>65</entry><entry>IIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGREKFLDKVWEWKDEY</entry><entry>124</entry></row><row><entry /><entry /><entry>I+IRQKR++GFDTLWLPGMDHAGIATQAKVE +LR++GISRYDLGREKF+ KVWEWKDE+</entry></row><row><entry>Sbjct:</entry><entry>87</entry><entry>IVIRQKRIEGFDTLWLPGMDHAGIATQAKVEAKLRKEGISRYDLGREKFVQKVWEWKDEF</entry><entry>146</entry></row><row><entry /></row><row><entry>Query:</entry><entry>125</entry><entry>AATIKSQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYNKGWIYRGEFIINWDPAART</entry><entry>184</entry></row><row><entry /><entry /><entry>A TI  QW KMGLS+DYSRERFTLD+GL++AVR+VFVDLYN+G IYRGE+I+NWDP ART</entry></row><row><entry>Sbjct:</entry><entry>147</entry><entry>AKTIHGQWAKMGLSLDYSRERFTLDKGLNQAVRRVFVDLYNQGLIYRGEYIVNWDPQART</entry><entry>206</entry></row><row><entry /></row><row><entry>Query:</entry><entry>185</entry><entry>ALSDIEVIHKDVEGAFYHMNYMLEDGSRALEVATTRPETMFGDVAVAVNPEDARYKDLIG</entry><entry>244</entry></row><row><entry /><entry /><entry>ALSDIEVIHKD +GAFYH+ Y   DGS  +E+ATTRPETM GD AVAV+P D RYKD++G</entry></row><row><entry>Sbjct:</entry><entry>207</entry><entry>ALSDIEVIHKDDKGAFYHVKYPFADGSGYIEIATTRPETMMGDTAVAVHPGDERYKDMVG</entry><entry>266</entry></row><row><entry /></row><row><entry>Query:</entry><entry>245</entry><entry>QNVILPIINKPIPIVADEHADPEFGTGVVKITPAHDPNDFAVGQRHNLPQVNVMNDDGTM</entry><entry>304</entry></row><row><entry /><entry /><entry>  +ILP+ N+ IPI+ D + DPEFGTG VKITPAHDPNDF VG RH+L ++N MNDDGTM</entry></row><row><entry>Sbjct:</entry><entry>267</entry><entry>TELILPLANRKIPIIEDAYVDPEFGTGAVKITPAHDPNDFQVGNRHDLKRINTMNDDGTM</entry><entry>326</entry></row><row><entry /></row><row><entry>Query:</entry><entry>305</entry><entry>NELADEFNGMDRFEARKAVVAKLESLGNLVKIKKTTHSVGHSERTGVVVEPRLSTQWFVK</entry><entry>364</entry></row><row><entry /><entry /><entry>NE A ++ GMDRFEARKA+VA L+  G L+K++   HSVGHSERTGV VE RLSTQWFVK</entry></row><row><entry>Sbjct:</entry><entry>327</entry><entry>NENAGKYQGMDRFEARKAMVADLDKAGLLLKVEPIVHSVGHSERTGVQVEARLSTQWFVK</entry><entry>386</entry></row><row><entry /></row><row><entry>Query:</entry><entry>365</entry><entry>MDQLAKNAI-ANQDTEDKVEFYPPRFNDTFMSWMENVHDWVISRQLWWGHQIPAWYN-VN</entry><entry>422</entry></row><row><entry /><entry /><entry>M  LA+ AI A Q+ + KV F P RF  T++ WMEN+HDWVISRQLWWGHQIPAWYN</entry></row><row><entry>Sbjct:</entry><entry>387</entry><entry>MKPLAEAAIKAQQEPDKKVTFVPERFEHTYLQWMENIHDWVISRQLWWGHQIPAWYNKQT</entry><entry>446</entry></row><row><entry /></row><row><entry>Query:</entry><entry>423</entry><entry>GEMYVGEDAPEG-DGWTQDEDVLDTWFSSALWPFSTMGWPDTEAADFKRYFPTSTLVTGY</entry><entry>481</entry></row><row><entry /><entry /><entry>GE YVG +AP+  + W QD DVLDTWFSSALWPFSTMGWP+T+A D+KRY+PT TLVTGY</entry></row><row><entry>Sbjct:</entry><entry>447</entry><entry>GETYVGMEAPKDIENWKQDPDVLDTWFSSALWPFSTMGWPNTDAPDYKRYYPTDTLVTGY</entry><entry>506</entry></row><row><entry /></row><row><entry>Query:</entry><entry>482</entry><entry>DIIFFWVSRMIFQSLEFTGRQPFSNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGAD</entry><entry>541</entry></row><row><entry /><entry /><entry>DII FWV+RMIFQ L FT ++PF   LIHGL+RDE+GRKMSKSLGNGIDPMDVIEKYGAD</entry></row><row><entry>Sbjct:</entry><entry>507</entry><entry>DIIPFWVARMIFQGLHFTHQRPFQYTLIHGLMRDEQGRKMSKSLGNGIDPMDVIEKYGAD</entry><entry>566</entry></row><row><entry /></row><row><entry>Query:</entry><entry>542</entry><entry>ALRWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLDQARENVEKVV</entry><entry>601</entry></row><row><entry /><entry /><entry>ALRWFL  G+ PGQD RFSY++++A+WNFINKIWNISR+++MN   L   Q  +</entry></row><row><entry>Sbjct:</entry><entry>567</entry><entry>ALRWFLITGNKPGQDTRFSYKQVEAAWNFINKIWNISRFVMMNLGDLDTPQQPD------</entry><entry>620</entry></row><row><entry /></row><row><entry>Query:</entry><entry>602</entry><entry>NSQVGNVTDRWILHNLNETVGKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLY</entry><entry>661</entry></row><row><entry /><entry /><entry>     +++D+W+   LNET+ +V +   +FEFG  G  LYNF W   A+WYVE++KEVLY</entry></row><row><entry>Sbjct:</entry><entry>621</entry><entry>-PSTFDLSDKWLFAQLNETIKQVMDLSARFEFGEMGRTLYNFTWNVLADWYVEMSKEVLY</entry><entry>679</entry></row><row><entry /></row><row><entry>Query:</entry><entry>662</entry><entry>SDNEDEKVITRSVLLYTLDQILRLLHPINPFVTEEIF--GQYAEGSIVLASYPQVNATFE</entry><entry>719</entry></row><row><entry /><entry /><entry> D+E  K   R  L Y LDQILRLLHP+NPFV  +++    +   SIV ASYP  N  FE</entry></row><row><entry>Sbjct:</entry><entry>680</entry><entry>GDDEQAKAAKRVNLAYALDQILRLLHPVMPFVHGKLWLALPHTGKSIVTASYPVANTAFE</entry><entry>739</entry></row><row><entry /></row><row><entry>Query:</entry><entry>720</entry><entry>NQTAHKGVESLKDLIRSVRNSRAEVNVAPSKPITILVKTSDSELESFFKDNSNYIKRFTN</entry><entry>779</entry></row><row><entry /><entry /><entry>N  A   ++++  LIR VR  R E        + ILVK +D  L+  F+ N ++I RF N</entry></row><row><entry>Sbjct:</entry><entry>740</entry><entry>NADATSAMDAIIALIRGVRGIRKEAGAPLKTKVDILVKLTDPALKPIFEQNFDFIDRFVN</entry><entry>799</entry></row><row><entry /></row><row><entry>Query:</entry><entry>780</entry><entry>PETLEISSAIATPELAMSSVITGAEIFLPLADLLNVEEELARLEKELAKWQKELDNVGKK</entry><entry>839</entry></row><row><entry /><entry /><entry> +   + + +A P++A S+VITGA IF+PL +L++++EE A+L K+  K ++E+  + KK</entry></row><row><entry>Sbjct:</entry><entry>800</entry><entry>SKAFTVGTDVAEPKMAGSAVITGATIFVPLNELIDLDEEKAKLTKDAKKLEQEIARIDKK</entry><entry>859</entry></row><row><entry /></row><row><entry>Query:</entry><entry>840</entry><entry>LSNERFVANAKPEVVQKEKDKQTDYQTKYDATIARIEEMKK</entry><entry>880</entry></row><row><entry /><entry /><entry>L+N+ F++ A   VV +++ K++D++ +  +T  R+E++++</entry></row><row><entry>Sbjct:</entry><entry>860</entry><entry>LNNQGFLSKAPEAVVAEQRTKRSDFEDQLTSTKQRLEQLQR</entry><entry>900</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 723&gt; which encodes the amino acid sequence &lt;SEQ ID 724&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00717" num="00717"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.5062 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00718" num="00718"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 782/878 (89%), Positives = 818/878 (93%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>4</entry><entry>ELSPKYNPAEVEEGRYQTWLDQDVFKPSGDTEAKPYSIVIPPPNVTGKLHLGHAWDTTLQ</entry><entry>63</entry><entry /></row><row><entry /><entry /><entry>ELSPKYNPAEVE GRYQ WLD DVFKPSGD +AKPYSIVIPPPNVTGKLHLGHAWDTTLQ</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>ELSPKYNPAEVEAGRYQKWLDADVFKPSGDQKAKPYSIVIPPPNVTGKLHLGHAWDTTLQ</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>64</entry><entry>DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGREKFLDKVWEWKDE</entry><entry>123</entry></row><row><entry /><entry /><entry>DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGR+KFLDKVWEWKDE</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGRDKFLDKVWEWKDE</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>124</entry><entry>YAATIKSQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYNKGWIYRGEFIINWDPAAR</entry><entry>183</entry></row><row><entry /><entry /><entry>YA TIK QWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLY KGWIYRGEFIINWDPAAR</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>YATTIKEQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYKKGWIYRGEFIINWDPAAR</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>184</entry><entry>TALSDIEVIHKDVEGAFYHMNYMLEDGSRALEVATTRPETMFGDVAVAVNPEDARYKDLI</entry><entry>243</entry></row><row><entry /><entry /><entry>TALSDIEVIHKDVEGAFYHMNYMLEDGSRAL+VATTRPETMFGDVAVAVNPED RYKDLI</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>TALSDIEVIHKDVEGAFYHMNYMLEDGSRALQVATTRPETMFGDVAVAVNPEDPRYKDLI</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>244</entry><entry>GQNVILPIINKPIPIVADEHADPEFGTGVVKITPAHDPNDFAVGQRHNLPQVNVMNDDGT</entry><entry>303</entry></row><row><entry /><entry /><entry>G+NVILPI+NK IPIV DEHADPEFGTGVVKITPAHDPNDF VGQRHNLPQVNVMNDDGT</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>GKNVILPIVNKLIPIVGDEHADPEFGTGVVKITPAHDPNDFEVGQRHNLPQVNVMNDDGT</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>304</entry><entry>MNELADEFNGMDRFEARKAVVAKLESLGNLVKIKKTTHSVGHSERTGVVVEPRLSTQWFV</entry><entry>363</entry></row><row><entry /><entry /><entry>MNELA +F GMDRFEAR+A VAKLE LG LV I+K  HSVGHSER+G VVEPRLSTQWFV</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>MNELAGDFAGMDRFEARQATVAKLEELGALVNIEKRVHSVGHSERSGAVVEPRLSTQWFV</entry><entry>362</entry></row><row><entry /></row><row><entry>Query:</entry><entry>364</entry><entry>KMDQLAKNAIANQDTEDKVEFYPPRFNDTFMSWMENVHDWVISRQLWWGHQIPAWYNVNG</entry><entry>423</entry></row><row><entry /><entry /><entry>KMD+LAK A+ NQ+T+D+V+FYPPRFNDTF+ WMENVHDWVISRQLWWGHQIPAWYN  G</entry></row><row><entry>Sbjct:</entry><entry>363</entry><entry>KMDELAKQAMDNQETDDRVDFYPPRFNDTFLQWMENVHDWVISRQLWWGHQIPAWYNAEG</entry><entry>422</entry></row><row><entry /></row><row><entry>Query:</entry><entry>424</entry><entry>EMYVGEDAPEGDGWTQDEDVLDTWFSSALWPFSTMGWPDTEAADFKRYFPTSTLVTGYDI</entry><entry>483</entry></row><row><entry /><entry /><entry>E+YVGE+APEGD WTQDEDVLDTWFSSALWPFSTMGWPDT+  DFKRYFPTSTLVTGYDI</entry></row><row><entry>Sbjct:</entry><entry>423</entry><entry>EIYVGEEAPEGDDWTQDEDVLDTWFSSALWPFSTMGWPDTDVEDFKRYFPTSTLVTGYDI</entry><entry>482</entry></row><row><entry /></row><row><entry>Query:</entry><entry>484</entry><entry>IFFWVSRMIFQSLEFTGRQPFSNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGADAL</entry><entry>543</entry></row><row><entry /><entry /><entry>IFFWVSRMIFQSLEFTGRQPF NVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGAD+L</entry></row><row><entry>Sbjct:</entry><entry>483</entry><entry>IFFWVSRMIFQSLEFTGRQPFQNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGADSL</entry><entry>542</entry></row><row><entry /></row><row><entry>Query:</entry><entry>544</entry><entry>RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLDQARENVEKVVNS</entry><entry>603</entry></row><row><entry /><entry /><entry>RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTL+ A  NV KV  S</entry></row><row><entry>Sbjct:</entry><entry>543</entry><entry>RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLEDAESNVAKVAAS</entry><entry>602</entry></row><row><entry /></row><row><entry>Query:</entry><entry>604</entry><entry>QVGNVTDRWILHNLNETVGKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD</entry><entry>663</entry></row><row><entry /><entry /><entry>+ GNVTD+WILHNLNET+ KVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD</entry></row><row><entry>Sbjct:</entry><entry>603</entry><entry>EAGNVTDQWILHNLNETIAKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD</entry><entry>662</entry></row><row><entry /></row><row><entry>Query:</entry><entry>664</entry><entry>NEDEKVITRSVLLYTLDQILRLLHPIMPFVTEEIFGQYAEGSIVLASYPQVNATFENQTA</entry><entry>723</entry></row><row><entry /><entry /><entry>NE EKVITRSVLLYTLD+ILRLLHPIMPFVTEEI+ QYA+GSIV   YP V   FEN+ A</entry></row><row><entry>Sbjct:</entry><entry>663</entry><entry>NEAEKVITRSVLLYTLDKILRLLHPIMPFVTEEIYAQYAQGSIVTVDYPVVRPAFENEAA</entry><entry>722</entry></row><row><entry /></row><row><entry>Query:</entry><entry>724</entry><entry>HKGVESLKDLIRSVRNSRAEVNVAPSKPITILVKTSDSELESFFKDNSNYIKRFTNPETL</entry><entry>783</entry></row><row><entry /><entry /><entry>HKGVESLKDLIR+VRN+RAEVNVAPSKPITILVKT+DSELE FF  N NYIK FTNPE L</entry></row><row><entry>Sbjct:</entry><entry>723</entry><entry>HKGVESLKDLIRAVRNARAEVNVAPSKPITILVKTADSELEDFFNSNINYIKCFTNPEKL</entry><entry>782</entry></row><row><entry /></row><row><entry>Query:</entry><entry>784</entry><entry>EISSAIATPELAMSSVITGAEIFLPLADLLNVEEELARLEKELAKWQKELDMVGKKLSNE</entry><entry>843</entry></row><row><entry /><entry /><entry>EISSAIA PELAM+S+ITGAEI+LPLADLLNVEEELARL+KELAKWQKELDMVGKKL NE</entry></row><row><entry>Sbjct:</entry><entry>783</entry><entry>EISSAIAAPELAMTSIITGAEIYLPLADLLNVEEELARLDKELAKWQKELDMVGKKLGNE</entry><entry>842</entry></row><row><entry /></row><row><entry>Query:</entry><entry>844</entry><entry>RFVANAKPEVVQKEKDKQTDYQTKYDATIARIEMKKL</entry><entry>881</entry></row><row><entry /><entry /><entry>RFVANAKPEVVQKEKDKQ DYQ KYDAT  RI EMKK+</entry></row><row><entry>Sbjct:</entry><entry>843</entry><entry>RFVANAKPEVVQKEKDKQADYQAKYDATQERIAEMKKI</entry><entry>880</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 228

A DNA sequence (GBSx0242) was identified in <i>S. agalactiae </i>&lt;SEQ ID 725&gt; which encodes the amino acid sequence &lt;SEQ ID 726&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00719" num="00719"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0669 (Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 727&gt; which encodes the amino acid sequence &lt;SEQ ID 728&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00720" num="00720"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 57</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>                bacterial outside --- Certainty = 0.3000(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00721" num="00721"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 148/191 (77%), Positives = 165/191 (85%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>14</entry><entry>GEKKKMNIIIIGAQASGKMTIGQEIAKQTGMTLFHNHDSIDFVLRFMPWSPDSIALTESI</entry><entry>73</entry><entry /></row><row><entry /><entry /><entry>G + KMN+IIIGAQASGKMTIGQE+A+QTGMTLFHNHDSIDFVLRFMPWS +S AL E I</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>GAETKMNLIIIGAQASGKMTIGQEVARQTGMTLFHNHDSIDFVLRFMPWSQESTALIERI</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>74</entry><entry>RFKFFETFAKTGQEMIFTIVIDFNDSRDVVFLEKIQIVFQSHNQEVLFVELETELSERLK</entry><entry>133</entry></row><row><entry /><entry /><entry>RF FFETFAKTGQ+MIFTIVIDFND  DV  LEKIQ VFQS++QEVLFVEL+T++ ERLK</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>RFAFFETFAKTGQDMIFTIVIDFNDPNDVAMLEKIQAVFQSYDQEVLFVELKTDIEERLK</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>134</entry><entry>RNRTENRLKHKPSKRDIKWSESDICSTMDYAIFNPEVAPEALTYYHKINNTCLTATETAY</entry><entry>193</entry></row><row><entry /><entry /><entry>RNRTENRLKHKP KR+I+WSE DI STM YA+FNPE  P+ LT+Y KINNT LTA ETA</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>RNRTENRLKHKPLKRNIEWSEQDIQSTMAYAVFNPEEPPKTLTHYQKINNTQLTAAETAQ</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>194</entry><entry>LIIQKINQIKE</entry><entry>204</entry></row><row><entry /><entry /><entry>LIIQK+  IKE</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>LIIQKMTHIKE</entry><entry>193</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 229

A DNA sequence (GBSx0243) was identified in <i>S. agalactiae </i>&lt;SEQ ID 729&gt; which encodes the amino acid sequence &lt;SEQ ID 730&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00722" num="00722"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3614(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00723" num="00723"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB04556 GB: AP001510 unknown conserved protein</entry><entry /></row><row><entry>[<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 60/189 (31%), Positives = 102/189 (53%), Gaps = 3/189 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>EIVDNQLPVVETNRLLLRQRKLEDAKEIFEFVKLDEVSYPAGFPAVKSLEEEITYIQEIY</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>E +   LP +ET RL LR+   +DA  I+++   ++V+    +   +S+++   ++   +</entry></row><row><entry>Sbjct:</entry><entry>4</entry><entry>EDIYGDLPTLETERLRLRKFYKDDAAAIYDYASNEQVTKYVLWETHQSIKDSEAFLA--F</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>PTNLEKEKLPSGYAITLKGDDKVIGSVDFNH-RHEDDIFEIGYLLHPDYWGQGIVPEAAS</entry><entry>125</entry></row><row><entry /><entry /><entry>  N   EK  S +AI LK ++++IG+VDF   + +D   E+GY+L   YWGQGI+ EA +</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>ALNKYDEKDVSPWAIELKRNERMIGTVDFVWWKPKDKTAELGYVLSEPYWGQGIMTEAVN</entry><entry>121</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>ALVEIGFTLLGLHKIELGCYDYNKQSQAVARKLGFTLEANIRDRRDAQGKRCGDMRFGLL</entry><entry>185</entry></row><row><entry /><entry /><entry>ALVE GF  + L +I+  C+  N  S  V  K G   E   R     +G       + ++</entry></row><row><entry>Sbjct:</entry><entry>122</entry><entry>ALVEFGFNNMELERIQAKCFAENISSARVMEKAGLIYEGTHRRAIYVKGAHRDFKVYAII</entry><entry>181</entry></row><row><entry /></row><row><entry>Query:</entry><entry>186</entry><entry>RSEWEKKRR</entry><entry>194</entry></row><row><entry /><entry /><entry>R ++E+K +</entry></row><row><entry>Sbjct:</entry><entry>182</entry><entry>REDYEQKHQ</entry><entry>190</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 731&gt; which encodes the amino acid sequence &lt;SEQ ID 732&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00724" num="00724"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1864(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00725" num="00725"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="308pt" align="left" /><colspec colname="2" colwidth="133pt" align="left" /><tbody valign="top"><row><entry>Identities = 50/58 (86%), Positives = 56/58 (96%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="252pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="133pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>137</entry><entry>LHKIELGCYDYNKQSQAVARKLGFTLEANIRDRRDAQGKRCGDMRFGLLRSEWEKKRR</entry><entry>194</entry><entry /></row><row><entry /><entry /><entry>LHKIELGCYDYNKQSQAVARKLGFTLEAN RDR+D QG+RCGDMRFGLLRSEWE++++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LHKIELGCYDYNKQSQAVARKLGFTLEANARDRKDVQGRRCGDMRFGLLRSEWEEQKQ</entry><entry>58</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 230

A DNA sequence (GBSx0244) was identified in <i>S. agalactiae </i>&lt;SEQ ID 733&gt; which encodes the amino acid sequence &lt;SEQ ID 734&gt;. This protein is predicted to be ribosomal-protein-alanine N-acetyltransferase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00726" num="00726"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4066(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9599&gt; which encodes amino acid sequence &lt;SEQ ID 9600&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00727" num="00727"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: BAB04418 GB: AP001509 ribosomal-protein-alanine</entry><entry /></row><row><entry>N-acetyltransferase [<i>Bacillus halodurans</i>]</entry></row><row><entry>Identities = 63/185 (34%), Positives = 95/185 (51%), Gaps = 11/185 (5%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>53</entry><entry>KALPKLETDRLILRQRTVGDVPAMFDYVCLEEVAYPAGLSPIASLEDEYDYFENRYYQNL</entry><entry>112</entry><entry /></row><row><entry /><entry /><entry>K  P LET RLILR+ T  D  ++  Y+  +EV    GL P  +LED     E  +Y+++</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>KRFPILETKRLILRKITTDDARSILSYLSDKEVMKYFGLEPFQTLEDALG--EIAWYESI</entry><entry>63</entry></row><row><entry /></row><row><entry>Query:</entry><entry>113</entry><entry>EKAKLPSGYGITVKGSDRIIGSCAFN-----HRHEDDVFEICYLLHPDYWGHGYMTEAVA</entry><entry>167</entry></row><row><entry /><entry /><entry>   +    +GIT+KG D +IGSC F+     H   +  FE+  L    YWG G  +EA+</entry></row><row><entry>Sbjct:</entry><entry>64</entry><entry>LHEQTGIRWGITLKGQDEVIGSCGFHQWVPKHHRAEIGFELSKL----YWGQGIASEAIR</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>168</entry><entry>ALIEVGFTLLNLHKIEIRCYDYNKQSRRVAEKLGFTLEATIRDRKDNQDNRCVNLIYGLL</entry><entry>227</entry></row><row><entry /><entry /><entry>A+I+ GF  L L +I+      N  S+R+ EK GF  E  +R  +          +Y LL</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>AVIQYGFEHLELQRIQALIEPPNIPSQRLVEKQGFISEGLLRSYEYTCGKFDDLYMYSLL</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>228</entry><entry>RSEWE</entry><entry>232</entry></row><row><entry /><entry /><entry>+ +++</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>KRDFD</entry><entry>184</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 732:

<tables id="TABLE-US-00728" num="00728"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="287pt" align="left" /><colspec colname="2" colwidth="154pt" align="left" /><tbody valign="top"><row><entry>Identities = 39/54 (72%), Positives = 44/54 (81%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="231pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="154pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>179</entry><entry>LHKIEIRCYDYNKQSRRVAEKLGFTLEATIRDRKDNQDNRCVNLIYGLLRSEWE</entry><entry>232</entry><entry /></row><row><entry /><entry /><entry>LHKIE+ CYDYNKQS+ VA KLGFTLEA  RDRKD Q  RC ++ +GLLRSEWE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>LHKIELGCYDYNKQSQAVARKLGFTLEANARDRKDVQGRRCGDMRFGLLRSEWE</entry><entry>54</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 231

A DNA sequence (GBSx0245) was identified in <i>S. agalactiae </i>&lt;SEQ ID 735&gt; which encodes the amino acid sequence &lt;SEQ ID 736&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00729" num="00729"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 51</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2719(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 232

A DNA sequence (GBSx0246) was identified in <i>S. agalactiae </i>&lt;SEQ ID 737&gt; which encodes the amino acid sequence &lt;SEQ ID 738&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00730" num="00730"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3250(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9597&gt; which encodes amino acid sequence &lt;SEQ ID 9598&gt; was also identified.

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 739&gt; which encodes the amino acid sequence &lt;SEQ ID 740&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00731" num="00731"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 38</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3293(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00732" num="00732"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="294pt" align="left" /><colspec colname="2" colwidth="147pt" align="left" /><tbody valign="top"><row><entry>Identities = 24/55 (43%), Positives = 38/55 (68%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="238pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="147pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>56</entry><entry>LLEGLTANKQDVLKEAGLVSLEAFAKVSEADVLALKGIGPAAIKQLVDNGVVFAK</entry><entry>110</entry><entry /></row><row><entry /><entry /><entry>++ G+ ++  + L   G+ S +AF + +E D+LALKGIGPA +K+LV+NG  F K</entry></row><row><entry>Sbjct:</entry><entry>77</entry><entry>VVAGIRSDLVETLYAEGIHSAQAFKEWTEKDLLALKGIGPATVKKLVENGASFKK</entry><entry>131</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 233

A DNA sequence (GBSx0247) was identified in <i>S. agalactiae </i>&lt;SEQ ID 741&gt; which encodes the amino acid sequence &lt;SEQ ID 742&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00733" num="00733"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 25</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2901(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 743&gt; which encodes the amino acid sequence &lt;SEQ ID 744&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00734" num="00734"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2536(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00735" num="00735"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 57/84 (67%), Positives = 73/84 (86%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSYEQEFLKDFEEWLQSQISINQMAMDSAKKVLEEDKDERAADAYIRYESKLDAYRFLQG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MSYE+EFLKDFE+W+++QI +NQ+AM ++++V +ED DERA DA+IRYESKLDAY FL G</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSYEKEFLKDFEDWVKTQIQVNQLAMATSQEVAQEDGDERAKDAFIRYESKLDAYEFLLG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KFNNYHNQKSFHDLPDGLFGQRHY</entry><entry>84</entry></row><row><entry /><entry /><entry>KF+NY N K+FHD+PD LFG RHY</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KFDNYKNGKAFHDIPDELFGARHY</entry><entry>84</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 234

A DNA sequence (GBSx0248) was identified in <i>S. agalactiae </i>&lt;SEQ ID 745&gt; which encodes the amino acid sequence &lt;SEQ ID 746&gt;. This protein is predicted to be methyltransferase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00736" num="00736"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 61</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.2469(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 747&gt; which encodes the amino acid sequence &lt;SEQ ID 748&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00737" num="00737"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3352(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00738" num="00738"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 26/60 (43%), Positives = 37/60 (61%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>23</entry><entry>LKNERCPHPKLINVLERKLEIILGDQKHILEKDSLISLSPQETHHLRAIENSKFLQIELD</entry><entry>82</entry><entry /></row><row><entry /><entry /><entry>+  E  P  K+I VLE +L   L DQK +L ++SLI++  Q+ HHL A  + K LQ+ LD</entry></row><row><entry>Sbjct:</entry><entry>42</entry><entry>ISQETSPRDKVILVLEGQLIFDLEDQKQVLTQESLIAIPAQKVHHLEAKTDCKLLQVLLD</entry><entry>101</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 235

A DNA sequence (GBSx0249) was identified in <i>S. agalactiae </i>&lt;SEQ ID 749&gt; which encodes the amino acid sequence &lt;SEQ ID 750&gt;. This protein is predicted to be integrase (codV). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00739" num="00739"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 59</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3842(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 236

A DNA sequence (GBSx0250) was identified in <i>S. agalactiae </i>&lt;SEQ ID 751&gt; which encodes the amino acid sequence &lt;SEQ ID 752&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00740" num="00740"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; May be a lipoprotein</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

SEQ ID 752 (GBS128) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 23</figref> (lane 5; MW 15 kDa). It was also expressed in <i>E. coli </i>as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 32</figref> (lane 4; 2 bands).

The GBS128-GST fusion product was purified (<figref idrefs="DRAWINGS">FIG. 198</figref>, lane 2) and used to immunise mice. The resulting antiserum was used for FACS (<figref idrefs="DRAWINGS">FIG. 288</figref>), which confirmed that the protein is immunoaccessible on GBS bacteria.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 237

A DNA sequence (GBSx0251) was identified in <i>S. agalactiae </i>&lt;SEQ ID 753&gt; which encodes the amino acid sequence &lt;SEQ ID 754&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00741" num="00741"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.2940 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 755&gt; which encodes the amino acid sequence &lt;SEQ ID 756&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00742" num="00742"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 42</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.2518 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00743" num="00743"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 10/90 (11%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="42pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:  3</entry><entry>TVAVRVDDQLKDDATELFQSLGLDMSTAVKMFLIQSVKTQSIPFEIK--------NKSSV</entry><entry>54</entry><entry /></row><row><entry /><entry>T+ +RVDD +K  A ++ + LG+ MSTA+ MFL Q + T  IPF++         N   +</entry></row><row><entry>Sbjct: 15</entry><entry>TLNLRVDDSVKSAADDILKRLGIPMSTAIDMFLNQIILTGGIPFDVSLPEAPQRVNVDYM</entry><entry>74</entry></row><row><entry /></row><row><entry>Query: 55</entry><entry>SDEEFQNLVETKLKGIRVKASDPESVNAFF</entry><entry>84</entry></row><row><entry /><entry>S E+F + + T  +    K  +P+ V  F+</entry></row><row><entry>Sbjct: 75</entry><entry>SQEKFYDKLITSFED--AKTCNPQDVGKFY</entry><entry>102</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 238

A DNA sequence (GBSx0252) was identified in <i>S. agalactiae </i>&lt;SEQ ID 757&gt; which encodes the amino acid sequence &lt;SEQ ID 758&gt;. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00744" num="00744"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="140pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −2.81</entry><entry>Transmembrane 370-386 (368-388)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry> bacterial membrane --- Certainty = 0.2126 (Affirmative) &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9593&gt; which encodes amino acid sequence &lt;SEQ ID 9594&gt; was also identified. A related GBS nucleic acid sequence &lt;SEQ ID 10773&gt; which encodes amino acid sequence &lt;SEQ ID 10774&gt; was also identified.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 759&gt; which encodes the amino acid sequence &lt;SEQ ID 760&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00745" num="00745"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 37</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="140pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −4.57</entry><entry>Transmembrane 354-370 (353-371)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry> bacterial membrane --- Certainty = 0.2826 (Affirmative) &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry /></row><row><entry>LPXTG motif: 344-348</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00746" num="00746"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 64/277 (23%), Positives = 99/277 (35%), Gaps = 31/277 (11%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query: 126</entry><entry>SIGNLPDLPKGTTVAFETPVDTATPGDKPAKVVVTYPDGSKDTVDVTVKVVDPRTDADKN</entry><entry>185</entry><entry /></row><row><entry /><entry>++ +LP   + TT   E PV         + V       + D+ + T     P   A</entry></row><row><entry>Sbjct: 121</entry><entry>AVKDLPASTESTTQPVEAPVQETQASASDSMVTGDSTSVTTDSPEETPSSESPVAPALSE</entry><entry>180</entry></row><row><entry /></row><row><entry>Query: 186</entry><entry>DPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVAFETPVDTATPGDKPAKVVVTYPDGSK</entry><entry>245</entry></row><row><entry /><entry> PA    Q    E P    S    P     T  A ETP + A P   P     +    S+</entry></row><row><entry>Sbjct: 181</entry><entry>APA----QPAESEEPSVAASSEETPS--PSTPAAPETPEEPAAPSPSPESEEPSVAAPSE</entry><entry>234</entry></row><row><entry /></row><row><entry>Query: 246</entry><entry>DTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVAFETPVDT</entry><entry>305</entry></row><row><entry /><entry>+T         P   A  + PA  ++      T  +       P  P  +    +TP</entry></row><row><entry>Sbjct: 235</entry><entry>ETPSPET----PEEPAAPSQPAESEESSVAATTSPS-------PSTPAESET--QTPPAV</entry><entry>281</entry></row><row><entry /></row><row><entry>Query: 306</entry><entry>ATPGDKPAKVVVTYPDGSKDTVDVTVKVVDPRTDADK----------NDPAGKDQQVNGK</entry><entry>355</entry></row><row><entry /><entry>    DKP+</entry><entry>     P  S    + TV+    +  +DK          N    +  + +</entry></row><row><entry>Sbjct: 282</entry><entry>TKDSDKPSSAAEK-PAASSLVSEQTVQQPTSKRSSDKKEEQEQSYSPNRSLSRQVRAHES</entry><entry>340</entry></row><row><entry /></row><row><entry>Query: 356</entry><entry>GNKLPATGENATPFFNVVALTIMSSVGLLSVSKKKED</entry><entry>392</entry></row><row><entry /><entry>G  LP+TGE A P F +  +T+MS  G L V+K++++</entry></row><row><entry>Sbjct: 341</entry><entry>GKYLPSTGEKAQPLF-IATMTLMSLFGSLLVTKRQKE</entry><entry>376</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 239

A DNA sequence (GBSx0253) was identified in <i>S. agalactiae </i>&lt;SEQ ID 761&gt; which encodes the amino acid sequence &lt;SEQ ID 762&gt;. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00747" num="00747"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.5289 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 240

A DNA sequence (GBSx0254) was identified in <i>S. agalactiae </i>&lt;SEQ ID 763&gt; which encodes the amino acid sequence &lt;SEQ ID 764&gt;. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00748" num="00748"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="133pt" align="left" /><colspec colname="4" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −1.06</entry><entry>Transmembrane 39-55 (39-55)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry> bacterial membrane --- Certainty = 0.1426 (Affirmative) &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9591&gt; which encodes amino acid sequence &lt;SEQ ID 9592&gt; was also identified.

The protein differs significantly from U58333 in several places:

<tables id="TABLE-US-00749" num="00749"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry><entry /></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>683</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>742</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>743</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>798</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>841</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>900</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>901</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>956</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>288</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>347</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>348</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>403</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>604</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>663</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>664</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>719</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>446</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>505</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>506</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>561</entry></row><row><entry /></row><row><entry>Query:</entry><entry>157</entry><entry>TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK</entry><entry>201</entry></row><row><entry /><entry /><entry>T PDG  D V+V++ + +     DK D   K          KAED     P   +G+</entry></row><row><entry>Sbjct:</entry><entry>920</entry><entry>TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA</entry><entry>979</entry></row><row><entry /></row><row><entry>Query:</entry><entry>202</entry><entry>VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV</entry><entry>258</entry></row><row><entry /><entry /><entry>    +D   T  D   K   T  D +    +VT   K++ PR  DADKNDPAGKDQQVNV</entry></row><row><entry>Sbjct:</entry><entry>980</entry><entry>FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV</entry><entry>1035</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 241

A DNA sequence (GBSx0255) was identified in <i>S. agalactiae </i>&lt;SEQ ID 765&gt; which encodes the amino acid sequence &lt;SEQ ID 766&gt;. This protein is predicted to be ara-C-like activator. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00750" num="00750"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 30</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="21pt" align="left" /><colspec colname="1" colwidth="63pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="77pt" align="left" /><colspec colname="4" colwidth="70pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −0.37</entry><entry>Transmembrane</entry><entry>8-24 (8-25)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1150(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9589&gt; which encodes amino acid sequence &lt;SEQ ID 9590&gt; was also identified.

There is homology to SEQ ID 460.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 242

A DNA sequence (GBSx0256) was identified in <i>S. agalactiae </i>&lt;SEQ ID 767&gt; which encodes the amino acid sequence &lt;SEQ ID 768&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00751" num="00751"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 53</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry><entry /></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1200(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9587&gt; which encodes amino acid sequence &lt;SEQ ID 9588&gt; was also identified.

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 769&gt; which encodes the amino acid sequence &lt;SEQ ID 770&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00752" num="00752"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 50</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0679 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00753" num="00753"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 135/176 (76%), Positives = 161/176 (90%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MSYMVKDRQIQKTKVAIYNAFISLLQENDYSKITVQDVIGLANVGRSTFYSHYESKEVLL</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>+S M KDRQI+KTK AIY+AFI+LLQ+ +YSKITV+D+I LANVGRSTFY+HYESKE+LL</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>VSDMTKDRQIKKTKTAIYSAFIALLQKKEYSKITVRDMITLANVGRSTFYAHYESKEMLL</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KELCEDLFHHLFKQGRDVTFEEYLVHILKHFEQNQDSIATLLLSDDPYFLLRFRSELEHD</entry><entry>120</entry></row><row><entry /><entry /><entry>KELCE+LFHHLF+Q R+VTFE+YLVHILKHFEQN+DSIATLLLS+DPYFLLRF++ELEHD</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KELCEELFHHLFRQKRNVTFEDYLVHILKHFEQNKDSIATLLLSNDPYFLLRFKNELEHD</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>VYPRLREEYITKVDIPEDFLKQFLLSSFIETLKWWLHQRQKMTVEDLLKYYLTMVE</entry><entry>176</entry></row><row><entry /><entry /><entry>VYP LR +YI K  IPE FLKQF+LSSFIETLKWWLHQRQ+M+  +LLKYYL +++</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>VYPNLRCKYIDKTTIPEVFLKQFVLSSFIETLKWWLHQRQRMSANELLKYYLELIK</entry><entry>176</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 243

A DNA sequence (GBSx0257) was identified in <i>S. agalactiae </i>&lt;SEQ ID 771&gt; which encodes the amino acid sequence &lt;SEQ ID 772&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00754" num="00754"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 29</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.3573 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 244

A DNA sequence (GBSx0258) was identified in <i>S. agalactiae </i>&lt;SEQ ID 773&gt; which encodes the amino acid sequence &lt;SEQ ID 774&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00755" num="00755"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="84pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −10.19</entry><entry>Transmembrane</entry><entry>112-128 (107-131)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −8.07</entry><entry>Transmembrane</entry><entry>  77-93 (71-97)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −6.10</entry><entry>Transmembrane</entry><entry>144-160 (138-165)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.03</entry><entry>Transmembrane</entry><entry>165-181 (164-182)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.5076 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 775&gt; which encodes the amino acid sequence &lt;SEQ ID 776&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00756" num="00756"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 35</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −9.13</entry><entry>Transmembrane</entry><entry>112-128 (107-130)</entry><entry /></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.89</entry><entry>Transmembrane</entry><entry>144-160 (138-163)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −5.47</entry><entry>Transmembrane</entry><entry>   7-23 (6-29)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −3.50</entry><entry>Transmembrane</entry><entry>  77-93 (74-94)</entry></row><row><entry>INTEGRAL</entry><entry>Likelihood = −2.07</entry><entry>Transmembrane</entry><entry>166-182 (165-183)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.4652 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00757" num="00757"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 212/287 (73%), Positives = 245/287 (84%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MTSNKKVAIAFILNISFSVLEFIFGSLFFSGAILADAVHDFGDAIAIGISATLEKKSKKD</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M ++KKV I FILN+SFS++EFIFG+LFFSGAILADAVHDFGDAIAIGISA LE+K+ K</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MPASKKVTIIFILNLSFSLIEFIFGTLFFSGAILADAVHDFGDAIAIGISAILERKAVKK</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>EDTIFSLGYKRFSLLGALITSLILISGSILVMIENIPKLWHPTPVNYHGMFILAVIAIII</entry><entry>120</entry></row><row><entry /><entry /><entry>E   FSLGYKRFSLLGAL T+LILISGS+LVMIE IPKLWHPT VNY GMF+LA+ AIII</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>ESPNFSLGYKRFSLLGALTTNLILISGSLLVMIETIPKLWHPTIVNYDGMFVLAIFAIII</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>NGLASFILHSGQSKHEEILSLHFLEDILGWLAIIVISLILNWKPLYILDPLLSVAISTFI</entry><entry>180</entry></row><row><entry /><entry /><entry>NG ASFI+HS Q+K+EEILSLHFLEDILGWLAII++SLIL WKP YILDPLLS+AI++FI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>NGFASFIIHSNQTKNEEILSLHFLEDILGWLAIIILSLILKWKPWYILDPLLSIAIASFI</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>181</entry><entry>LSKALPKLLSTLKLFLDGVPDSIDYAALHDELKGLSQVRSINQLNIWSMDGIDNRAIIHC</entry><entry>240</entry></row><row><entry /><entry /><entry>LSKALPKL++T  +FLDGVPDSIDY  LH EL  L  + S+NQLN+WSMDGID+RA IHC</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>LSKALPKLVATANIFLDGVPDSIDYCTLHHELSQLPHIVSVNQLNVWSMDGIDHRATIHC</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>241</entry><entry>CLNQLISEKDCKRAIRTICQHYKINDVTVEIDYSLREHQNHCKPLKN</entry><entry>287</entry></row><row><entry /><entry /><entry>CL +  +EK CK++IR ICQ Y IN VTVEID SL EHQ+HC  L +</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>CLRESTTEKHCKKSIRLICQRYNINSVTVEIDTSLNENQHHCSSLSS</entry><entry>287</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 245

A DNA sequence (GBSx0259) was identified in <i>S. agalactiae </i>&lt;SEQ ID 777&gt; which encodes the amino acid sequence &lt;SEQ ID 778&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00758" num="00758"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="35pt" align="left" /><colspec colname="2" colwidth="77pt" align="left" /><colspec colname="3" colwidth="56pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>INTEGRAL</entry><entry>Likelihood = −1.22</entry><entry>Transmembrane</entry><entry>221-237 (221-237)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>bacterial membrane --- Certainty = 0.1489 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 780.

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 246

A DNA sequence (GBSx0260) was identified in <i>S. agalactiae </i>&lt;SEQ ID 781&gt; which encodes the amino acid sequence &lt;SEQ ID 782&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00759" num="00759"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 13</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −2.50</entry><entry>Transmembrane</entry><entry>2-18 (1-18)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.1999(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 247

A DNA sequence (GBSx0261) was identified in <i>S. agalactiae </i>&lt;SEQ ID 783&gt; which encodes the amino acid sequence &lt;SEQ ID 784&gt;. This protein is predicted to be dehydrogenase (Zn-dependent). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00760" num="00760"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 15</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −3.77</entry><entry>Transmembrane</entry><entry>171-187 (170-187)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.2508(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00761" num="00761"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAG20655 GB:AE005134 alcohol dehydrogenase; Adh2 [<i>Halobacterium </i>sp. NRC-1]</entry><entry /></row><row><entry>Identities = 169/348 (48%), Positives = 232/348 (66%), Gaps = 9/348 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MKVATFIEPGKMVITDTPKPVIEQETDAVIKIVRACVCGSDLWWYRGISKRESGSFAGHE</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+ A +  PG++ + + PKP IE   DAVI++    VCGSDLW+YRG S RE+GS  GHE</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MRAAVYQGPGEIAVEEVPKPDIESPEDAVIRVTHTAVCGSDLWFYRGDSDREAGSRVGHE</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>AIGIVEEVGTKVTDVSKGDFVIVPFTHGCGQCPSCKAGFDGNCTNHQA---AKNVGYQGQ</entry><entry>117</entry></row><row><entry /><entry /><entry> +GIVEEVG  VT V+ GD VI PF   CG+C  C+ G   +C   ++     N G QG+</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>PMGIVEEVGDDVTSVAPGDRVIAPFAISCGECEFCRQGLYTSCVEDESWGSEANGGGQGE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>118</entry><entry>YLRYTNANWALVKIPGQPSDYDNETLNSLLTLSDVMATGYHAAATAEVKEGDTVVVMGDG</entry><entry>177</entry></row><row><entry /><entry /><entry>Y++   A+  LV++P + +D D + L SLL L+DVM TG+HAA +A V EGDT VV+GDG</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>YVKCPFADGTLVRVPDRYAD-DEDVLESLLPLTDVMGTGHHAAVSAGVGEGDTAVVVGDG</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>178</entry><entry>AVGLCGVIAAKMLGANRIIAMSRHKDRQELALTFGATDIVEERGDEAVKRVLDLTNQAGA</entry><entry>237</entry></row><row><entry /><entry /><entry>AVGLCGV+AA+ LGA RIIAM  H+DR ELA  FGATD +  RGD+A++R  DLT+  GA</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>AVGLCGVLAAQRLGAERIIAMGHHEDRLELAAEFGATDTISARGDDAIERARDLTH-GGA</entry><entry>238</entry></row><row><entry /></row><row><entry>Query:</entry><entry>238</entry><entry>DAVLECVGTEQSVDTATQIARPGAVIGRVGIP---QNPDMNTNNLFWKNIGLRGGIASVT</entry><entry>294</entry></row><row><entry /><entry /><entry>+ V+ECVG   ++D+A  IARPG  +G VG+P   ++  ++   +F  NI +RGG+A V</entry></row><row><entry>Sbjct:</entry><entry>239</entry><entry>NHVMECVGAASAMDSAIAIARPGGTVGYVGVPYGVEDGGLDVFTMFSDNITIRGGVAPVR</entry><entry>298</entry></row><row><entry /></row><row><entry>Query:</entry><entry>295</entry><entry>TFDKSVLLDAVLTHKINPGLVFTKSFVLDDIQKAYEAMDKRDAIKSLV</entry><entry>342</entry></row><row><entry /><entry /><entry> + + ++ D VL   ++P  +FTK+  LD + + Y AMD R+AIK LV</entry></row><row><entry>Sbjct:</entry><entry>299</entry><entry>AYAEELMAD-VLQGTLDPSPIFTKTVDLDGVPEGYAAMDDREAIKVLV</entry><entry>345</entry></row></tbody></tgroup></table></tables>

There is also homology to SEQ ID 786.

A related sequence was also identified in GAS &lt;SEQ ID 9145&gt; which encodes the amino acid sequence &lt;SEQ ID 9146&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00762" num="00762"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 23</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="98pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.41</entry><entry>Transmembrane</entry><entry>170-186</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3166(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00763" num="00763"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Identities = 121/353 (34%), Positives = 182/353 (51%), Gaps = 16/353 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:   1</entry><entry>MKVATFIEPGKMVITDTPKPVIEQETDAVIKIVRACVCGSDLWWYRG-ISKRESGSFAGH</entry><entry>59</entry><entry /></row><row><entry /><entry>MK AT++  G + + D PKPVI + TDA++++V+  + CG+DL    G +   + G+  GH</entry></row><row><entry>Sbjct:  15</entry><entry>MKAATYLSTGNLQLIDKPKPVIIKPTDAIVQLVKTTICGTDLHILGGDVPACKEGTILGH</entry><entry>74</entry></row><row><entry /></row><row><entry>Query:  60</entry><entry>EAIGIVEEVGTKVTDVSKGDFVIVPFTHGCGQCPSCKAGFDGNCTNHQAAKN---VGYQG</entry><entry>116</entry></row><row><entry /><entry>E IGIV+EVG  VT+   GD VI+     C  C  CK G   +C +          G Q</entry></row><row><entry>Sbjct:  75</entry><entry>EGIGIVKEVGDAVTNFKIGDKVIISCVTSCHTCYYCKRGLSSHCQDGGWILGHLINGTQA</entry><entry>134</entry></row><row><entry /></row><row><entry>Query: 117</entry><entry>QYLRYTNANWALVKIPGQPSDYDNETLNSLLTLSDVMATGYH-AAATAEVKEGDTVVVMG</entry><entry>175</entry></row><row><entry /><entry>+Y+   +A+ +L   P    D       +L+ LSD++ T Y      + VK  GD V ++G</entry></row><row><entry>Sbjct: 135</entry><entry>EYVHIPHADGSLYHAPDTIDD------EALVMLSDILPTSYEIGVLPSHVKPGDNVCIVG</entry><entry>188</entry></row><row><entry /></row><row><entry>Query: 176</entry><entry>DGAVGLCGVIAAKMLGANRIIAMSRHKDRQELALTFGATDIVEERGDEAVKRVL-DLTNQ</entry><entry>234</entry></row><row><entry /><entry> G VGL  ++  +      II +   ++R E A TFGAT  +     E VK ++ D+TN</entry></row><row><entry>Sbjct: 189</entry><entry>AGPVGLAALLTVQFFSPANIIMVDLSQNRLEAAKTFGATHTICSGSSEEVKAIIDDITNG</entry><entry>248</entry></row><row><entry /></row><row><entry>Query: 235</entry><entry>AGADAVLECVGTEQSVDTATQIARPGAVIGRVGIPQNP-DMNTNNLFWKNIGLRGGIASV</entry><entry>293</entry></row><row><entry /><entry> G D  +ECVG   + D   +I   G  I  VG+   P  D N + L+ KNI L  G+ +</entry></row><row><entry>Sbjct: 249</entry><entry>RGVDISMECVGYPATFDICQKIISVGGHIANVGVHGKPVDFNLDELWIKNITLNTGLVNA</entry><entry>308</entry></row><row><entry /></row><row><entry>Query: 294</entry><entry>TTFDKSVLLDAVLTHKINPGLVFTKSFVLDDIQKAYEAMDKRDAIKSL-VIVD</entry><entry>345</entry></row><row><entry /><entry>T +   +LL+ + T KI+   + T  F L +++KAYE      A  +L VI+D</entry></row><row><entry>Sbjct: 309</entry><entry>NTTE--MLLNVLKTGKIDATRLITHHFKLSEVEKAYETFKHAGANNALKVIID</entry><entry>359</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 248

A DNA sequence (GBSx0262) was identified in <i>S. agalactiae </i>&lt;SEQ ID 787&gt; which encodes the amino acid sequence &lt;SEQ ID 788&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00764" num="00764"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 31</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.2169 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00765" num="00765"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAD36075 GB:AE001762 hypothetical protein [<i>Thermotoga maritima</i>]</entry><entry /></row><row><entry>Identities = 55/128 (42%), Positives = 72/128 (55%), Gaps = 8/128 (6%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:   8</entry><entry>IFPKGEKNPYGEFFIGQSYLAALAKSPDG--NVSVGNVTFEAGCRNNWHVHLDGYQILLV</entry><entry>65</entry><entry /></row><row><entry /><entry>IF +G K    +FF G  ++  L    +G  N  V +V FE G R +WH H  G QIL+V</entry></row><row><entry>Sbjct:   5</entry><entry>IFERGSKGS-SDFFTGNVWVKMLVTDENGVFNTQVYDVVFEPGARTHWHSHPGG-QILIV</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:  66</entry><entry>TEGSGWYQEEGKEAVSLKPGDVIVTDKGVRHWHGAKKDSEFAHIAITA----GKSEFYEA</entry><entry>121</entry></row><row><entry /><entry>T G G+YQE GK A  LK GDV+     V HWHGA  D E  HI I+     G +E+  +</entry></row><row><entry>Sbjct:  63</entry><entry>TRGKGFYQERGKPARILKKGDVVEIPPNVVHWHGAAPDEELVHIGISTQVHLGPAEWLGS</entry><entry>122</entry></row><row><entry /></row><row><entry>Query: 122</entry><entry>VSDEEYSR</entry><entry>129</entry></row><row><entry /><entry>V++EEY +</entry></row><row><entry>Sbjct: 123</entry><entry>VTEEEYRK</entry><entry>130</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 249

A DNA sequence (GBSx0263) was identified in <i>S. agalactiae </i>&lt;SEQ ID 789&gt; which encodes the amino acid sequence &lt;SEQ ID 790&gt;. This protein is predicted to be gamma-carboxymuconolactone decarboxylase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00766" num="00766"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 49</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.4089 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00767" num="00767"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:CAA20070 GB:AL031155 3-oxoadipate enol-lactone hydrolase/</entry><entry /></row><row><entry>4-carboxymuconolactone decarboxylase [<i>Streptomyces coelicolor</i> A3(2)]</entry></row><row><entry>Identities = 33/93 (35%), Positives = 59/93 (62%), Gaps = 1/93 (1%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="4"><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="259pt" align="left" /><colspec colname="3" colwidth="14pt" align="char" char="." /><colspec colname="4" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Query:  11</entry><entry>QLEEFAPEFARYNDDILFGEVWAKEDHLTDKTRSIITISALISGGNLEQLEHHLQFAKQN</entry><entry>70</entry><entry /></row><row><entry /><entry>Q +EF+ +F  +     +GE+W +   L  ++RS  +T++AL++GG+L++L  HL+ A +N</entry></row><row><entry>Sbjct: 349</entry><entry>QADEFSGDFQEFLTRYAWGEIWDRPG-LDRRSRSCVTLTALVAGGHLDELAPHLRAALRN</entry><entry>407</entry></row><row><entry /></row><row><entry>Query:  71</entry><entry>GVTKEEIADIITHLAFYVGWPKAWSAFNKAKEI</entry><entry>103</entry></row><row><entry /><entry>G+T  EI+++    A Y G P A  AF  A+++</entry></row><row><entry>Sbjct: 408</entry><entry>GLTPGEIKEVLLQAAVYCGVPAANGAFRVAQQV</entry><entry>440</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 250

A DNA sequence (GBSx0265) was identified in <i>S. agalactiae </i>&lt;SEQ ID 791&gt; which encodes the amino acid sequence &lt;SEQ ID 792&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00768" num="00768"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="273pt" align="left" /><colspec colname="2" colwidth="168pt" align="left" /><tbody valign="top"><row><entry>Possible site: 44</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.5529 (Affirmative) &lt;succ&gt;</entry></row><row><entry> bacterial membrane --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row><row><entry>  bacterial outside --- Certainty = 0.0000 (Not Clear)   &lt;succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has no significant homology with any sequences in the GENPEPT database.

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 251

A DNA sequence (GBSx0266) was identified in <i>S. agalactiae </i>&lt;SEQ ID 793&gt; which encodes the amino acid sequence &lt;SEQ ID 794&gt;. This protein is predicted to be probable transcriptional regulator. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00769" num="00769"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="322pt" align="left" /><colspec colname="2" colwidth="119pt" align="left" /><tbody valign="top"><row><entry>Possible site: 58</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have an uncleavable N-term signal seq</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

A related GBS nucleic acid sequence &lt;SEQ ID 9585&gt; which encodes amino acid sequence &lt;SEQ ID 9586&gt; was also identified.

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00770" num="00770"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAG08263 GB: AE004901 probable transcriptional regulator</entry><entry /></row><row><entry>[<i>Pseudomonas aeruginosa</i>]</entry></row><row><entry>Identities = 36/148 (24%), Positives = 68/148 (45%), Gaps = 22/148 (14%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>5</entry><entry>QIVEKPAMILAG-------------------VTLENVKSNQEGIQQAIGICKTQPDFRFD</entry><entry>45</entry><entry /></row><row><entry /><entry /><entry>+IVE+PA  + G                   +  E+  + +   + + GIC  QP+  F</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>RIVERPAFSVVGMEYFGSAPGDTIGQLWERFIPREHEIAGKHDPEVSYGICAQQPNGEFH</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>46</entry><entry>YSATYQVETSVQAPKGLEIIRIPSATYAVISVKGPMPSSLQETWRKIIQGFFQENNLKPA</entry><entry>105</entry></row><row><entry /><entry /><entry>Y A ++V+     P+G+   ++P+  YAV + KG  P  + E+++ I      E  L+P</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>YVAGFEVQEGWPVPEGMVRFQVPAQKYAVFTHKGTAP-QIAESFQAIYSHLLAERGLEPK</entry><entry>241</entry></row><row><entry /></row><row><entry>Query:</entry><entry>106</entry><entry>NSPNLEIYSSQH--PQDTDYQMEIWLAI</entry><entry>131</entry></row><row><entry /><entry /><entry>   + E Y  +   P D + Q+++++ I</entry></row><row><entry>Sbjct:</entry><entry>242</entry><entry>AGVDFEYYDQRFRGPLDPNSQVDLYIPI</entry><entry>269</entry></row></tbody></tgroup></table></tables>

No corresponding DNA sequence was identified in <i>S. pyogenes. </i>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 252

A DNA sequence (GBSx0267) was identified in <i>S. agalactiae </i>&lt;SEQ ID 795&gt; which encodes the amino acid sequence &lt;SEQ ID 796&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00771" num="00771"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0887(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00772" num="00772"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP: AAB84919 GB: AE000825 conserved protein [<i>Methanothermobacter</i></entry><entry /></row><row><entry><i>thermoautotrophicus</i>]</entry></row><row><entry>Identities = 42/130 (32%), Positives = 71/130 (54%), Gaps = 3/130 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MITQEMKEIINSQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>M+T EM + I  +L  VAT D +G PN+ P    R  D++T +  +N   +T  N+ +N</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MMTPEMMDAIEKELVFVATADEEGTPNVVPIGFARPLDERTILIADNYMKKTIRNLHENP</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KIEIAFVDRERLLGYRFVGTAEIQTEGTYYEAAKKWAEGRMG--VPKAVGIIHVERIFNL</entry><entry>118</entry></row><row><entry /><entry /><entry>+I +      R   Y+F GT EI   G Y++   +WA+  M    PK+  ++ VE I+++</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>RIAL-IPQNARECPYQFKGTVEIFKSGKYFDMVVEWAQNVMTELEPKSAILMTVEEIYSV</entry><entry>119</entry></row><row><entry /></row><row><entry>Query:</entry><entry>119</entry><entry>QSGANAGKEI</entry><entry>128</entry></row><row><entry /><entry /><entry>+ G  AG+++</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>KPGPEAGEKV</entry><entry>129</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 797&gt; which encodes the amino acid sequence &lt;SEQ ID 798&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00773" num="00773"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 24</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0789(Affirmative) &lt; succ&gt;</entry></row><row><entry>               bacterial membrane --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00774" num="00774"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 123/128 (96%), Positives = 127/128 (99%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>MITQEMKEIINSQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG</entry><entry>60</entry><entry /></row><row><entry /><entry /><entry>MITQEMK++IN+QLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MITQEMKDLINNQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>61</entry><entry>KIEIAFVDRERLLGYRFVGTAEIQTEGTYYEAAKKWAEGRMGVPKAVGIIHVERIFNLQS</entry><entry>120</entry></row><row><entry /><entry /><entry>KIEIAFVDRERLLGYRFVGTAEIQTEG YYEAAKKWA+GRMGVPKAVGIIHVERIFNLQS</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>KIEIAFVDRERLLGYRFVGTAEIQTEGAYYEAAKKWAQGRMGVPKAVGIIHVERIFNLQS</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>121</entry><entry>GANAGKEI</entry><entry>128</entry></row><row><entry /><entry /><entry>GANAGKEI</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>GANAGKEI</entry><entry>128</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 253

A DNA sequence (GBSx0268) was identified in <i>S. agalactiae </i>&lt;SEQ ID 799&gt; which encodes the amino acid sequence &lt;SEQ ID 800&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00775" num="00775"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Possible site: 22</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="6"><colspec colname="offset" colwidth="14pt" align="left" /><colspec colname="1" colwidth="49pt" align="left" /><colspec colname="2" colwidth="91pt" align="left" /><colspec colname="3" colwidth="70pt" align="left" /><colspec colname="4" colwidth="105pt" align="left" /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry /><entry>INTEGRAL</entry><entry>Likelihood = −5.47</entry><entry>Transmembrane</entry><entry>1028-1044 (1027-1048)</entry><entry /></row><row><entry /><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>----- Final Results -----</entry><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.3187(Affirmative) &lt; succ&gt;</entry></row><row><entry>                bacterial outside --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000(Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00776" num="00776"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>!GB: AF054892 surface antigen BspA [<i>Bacteroides forsy </i>. . .</entry><entry /></row><row><entry>!GB: AF054892 surface antigen BspA [<i>Bacteroides forsy </i>. . .</entry></row><row><entry>!GB: AF054892 surface antigen BspA [<i>Bacteroides forsy </i>. . .</entry></row><row><entry>!GB: AF054892 surface antigen BspA [<i>Bacteroides forsy </i>. . .</entry></row><row><entry>!GB: AF054892 surface antigen BspA [<i>Bacteroides forsy </i>. . .</entry></row><row><entry>&gt;GP: AAC82625 GB: AF054892 surface antigen BspA [<i>Bacteroides</i></entry></row><row><entry><i>forsythus</i>]</entry></row><row><entry>Identities = 143/566 (25%), Positives = 243/566 (42%), Gaps = 52/566 (9%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>95</entry><entry>VPKAKPEVTQEASNSSNDASKVEVPKQDTASKKETLETSTWEAKDFVTRGDTLVG----F</entry><entry>150</entry><entry /></row><row><entry /><entry /><entry>+P +   + + A    +    + +P   TA  +  L   T      +    T +G    F</entry></row><row><entry>Sbjct:</entry><entry>120</entry><entry>IPNSVTTIGEWAFKGCSGLKSITLPNSLTAIGQSALSGCTGLTSITIPNSVTTIGEWAFF</entry><entry>179</entry></row><row><entry /></row><row><entry>Query:</entry><entry>151</entry><entry>SKSGINKLSQTSHLVLPSHAA--DGTQLTQVASFAFTPDKKTAIAEYTSRLGENGKPSRL</entry><entry>208</entry></row><row><entry /><entry /><entry>  SG+  ++  + L     +A      LT +      PD  T I E   + G +G  S</entry></row><row><entry>Sbjct:</entry><entry>180</entry><entry>GCSGLTSITFPNSLTAIGESAFYGCGALTSIT----LPDALTTIGESAFK-GCSGLKSIT</entry><entry>234</entry></row><row><entry /></row><row><entry>Query:</entry><entry>209</entry><entry>DIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFA</entry><entry>268</entry></row><row><entry /><entry /><entry>  +    I E   ++   LT +T+P+   +IG+ AF     +  +  P SL TI + AF</entry></row><row><entry>Sbjct:</entry><entry>235</entry><entry>FPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGLKSITFPNSLTTIGESAFY</entry><entry>294</entry></row><row><entry /></row><row><entry>Query:</entry><entry>269</entry><entry>HM-SLKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKL</entry><entry>327</entry></row><row><entry /><entry /><entry>+  SL  + +P+++  IG  AF+       + LP  L  + ERAF +  + T   + + +</entry></row><row><entry>Sbjct:</entry><entry>295</entry><entry>NCGSLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLTSITIPNSV</entry><entry>354</entry></row><row><entry /></row><row><entry>Query:</entry><entry>328</entry><entry>KVIGEASFQD-NNLRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRTRTGQNPHQLATE</entry><entry>386</entry></row><row><entry /><entry /><entry>  IGE++F   + L+++ LPDGL  IE  AF          N   L + T  N      E</entry></row><row><entry>Sbjct:</entry><entry>355</entry><entry>ATIGESAFYGCSGLKSITLPDGLTTIEWGAFY---------NCGALTSITIPNSVSTIGE</entry><entry>405</entry></row><row><entry /></row><row><entry>Query:</entry><entry>387</entry><entry>NTYVNPDKSLWRATPDMDYTKWLEEDFTYQKNSVTGFS---NKGLQKVRRNKNLEIPKQH</entry><entry>443</entry></row><row><entry /><entry /><entry>+ +     +L   T   D    ++ D  +++ +++G       G + V   K  ++ K+</entry></row><row><entry>Sbjct:</entry><entry>406</entry><entry>SAFYGCG-ALKDVTVAWDTPIDIQRD-VFRELTLSGIRLHVPAGKKTVYEAK--DVWKEF</entry><entry>461</entry></row><row><entry /></row><row><entry>Query:</entry><entry>444</entry><entry>NGITITEIGDNAFRNVDFQSKTLRKYDLEEIKLPSTIRKIGAFAFQSNNLKSFEASEDLE</entry><entry>503</entry></row><row><entry /><entry /><entry>N +   + G   + N D  +KTL   +      P T + +  FA  ++ L</entry></row><row><entry>Sbjct:</entry><entry>462</entry><entry>NIVEDDDFGGLQW-NYDAATKTLTITN----PTPDTPKPMPNFATPNDQLW---------</entry><entry>507</entry></row><row><entry /></row><row><entry>Query:</entry><entry>504</entry><entry>EIKEGAFMNNRIGTLDLKDKLIKIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGALHL</entry><entry>562</entry></row><row><entry /><entry /><entry>    GAF    I  + + D +  +GD AF   + + +I LP+SV  IG+SAF     L</entry></row><row><entry>Sbjct:</entry><entry>508</entry><entry>----GAFQKE-IQKITIGDGVTSVGDFAFSGCDALKSITLPKSVTTIGQSAFSGCWDLRS</entry><entry>562</entry></row><row><entry /></row><row><entry>Query:</entry><entry>563</entry><entry>MFIGNKVKTIGEMAFLSNKLESVNLSEQKQLKTIEVQAFS-DNALSEVVLPPNLQTIREE</entry><entry>621</entry></row><row><entry /><entry /><entry>+ + + V TIGE AF  + LE  +++  K +  I  + F    +L+ + LP  L  I ++</entry></row><row><entry>Sbjct:</entry><entry>563</entry><entry>LTLPDGVNTIGEKAFY-DCLELTSITIPKSVTAIGQETFHYCVSLTSLTLPDALTAIGKK</entry><entry>621</entry></row><row><entry /></row><row><entry>Query:</entry><entry>622</entry><entry>AF-KRNHLKEVKGSSTLSQITFNAFD</entry><entry>646</entry></row><row><entry /><entry /><entry>AF   N L  V    +++ I  NAFD</entry></row><row><entry>Sbjct:</entry><entry>622</entry><entry>AFYSCNALTSVTFPKSITTIGENAFD</entry><entry>647</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 109/407 (26%), Positives = 175/407 (42%),</entry><entry /></row><row><entry>Gaps = 48/407 (11%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>222</entry><entry>FNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFAHMS-LKQVKLPDN</entry><entry>280</entry><entry /></row><row><entry /><entry /><entry>F+   LT +T+PN   +IG  AF     +  + +P S+ TI ++AF   S LK + LP++</entry></row><row><entry>Sbjct:</entry><entry>87</entry><entry>FSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNS</entry><entry>146</entry></row><row><entry /></row><row><entry>Query:</entry><entry>281</entry><entry>LKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQD-NN</entry><entry>339</entry></row><row><entry /><entry /><entry>L  IG+ A         + +P  +  + E AF      T     + L  IGE++F</entry></row><row><entry>Sbjct:</entry><entry>147</entry><entry>LTAIGQSALSGCTGLTSITIPNSVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGA</entry><entry>206</entry></row><row><entry /></row><row><entry>Query:</entry><entry>340</entry><entry>LRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRTRTGQNPHQLATENTYVNPDKSLWRA</entry><entry>399</entry></row><row><entry /><entry /><entry>L ++ LPD L  I   AF G  G         L++ T  N      E+ + +</entry></row><row><entry>Sbjct:</entry><entry>207</entry><entry>LTSITLPDALTTIGESAFKGCSG---------LKSITFPNSLTTIGESAFYDCGALTSIT</entry><entry>257</entry></row><row><entry /></row><row><entry>Query:</entry><entry>400</entry><entry>TPDMDYTKWLEEDFTYQKNSVTGFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNV</entry><entry>459</entry></row><row><entry /><entry /><entry> PD                ++T             K++  P      ++T IG++AF N</entry></row><row><entry>Sbjct:</entry><entry>258</entry><entry>LPD----------------ALTTIGRSAFYGCSGLKSITFPN-----SLTTIGESAFYNC</entry><entry>296</entry></row><row><entry /></row><row><entry>Query:</entry><entry>460</entry><entry>DFQSKTLRKYDLEEIKLPSTIRKIGAFAFQS-NNLKSFEASEDLEEIKEGAFMNNRIGT-</entry><entry>517</entry></row><row><entry /><entry /><entry>           L  I +P+++  IG  AF   + LKS    + L  I+E AF N  + T</entry></row><row><entry>Sbjct:</entry><entry>297</entry><entry>G---------SLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLTS</entry><entry>347</entry></row><row><entry /></row><row><entry>Query:</entry><entry>518</entry><entry>LDLKDKLIKIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMA</entry><entry>576</entry></row><row><entry /><entry /><entry>+ + + +  IG++AF+  + + +I LP+ +  I   AF   GAL  + I N V TIGE A</entry></row><row><entry>Sbjct:</entry><entry>348</entry><entry>ITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAFYNCGALTSITIPNSVSTIGESA</entry><entry>407</entry></row><row><entry /></row><row><entry>Query:</entry><entry>577</entry><entry>FLS-NKLESVNLSEQKQLKTIEVQAFSDNALSEVVL--PPNLQTIRE</entry><entry>620</entry></row><row><entry /><entry /><entry>F     L+ V ++    +  I+   F +  LS + L  P   +T+ E</entry></row><row><entry>Sbjct:</entry><entry>408</entry><entry>FYGCGALKDVTVAWDTPI-DIQRDVFRELTLSGIRLHVPAGKKTVYE</entry><entry>453</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 111/465 (23%), Positives = 185/465 (38%),</entry><entry /></row><row><entry>Gaps = 56/465 (12%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>141</entry><entry>VTRGDTLVGFSKSGINKLSQTSHLVLPSHAADGTQLTQVASFAF----------TPDKKT</entry><entry>190</entry><entry /></row><row><entry /><entry /><entry>+T  D L    +S     S    +  P+       LT +   AF           PD  T</entry></row><row><entry>Sbjct:</entry><entry>210</entry><entry>ITLPDALTTIGESAFKGCSGLKSITFPN------SLTTIGESAFYDCGALTSITLPDALT</entry><entry>263</entry></row><row><entry /></row><row><entry>Query:</entry><entry>191</entry><entry>AIAEYTSRLGENGKPSRLDIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNI</entry><entry>250</entry></row><row><entry /><entry /><entry> I   ++  G +G  S    +    I E   +N   LT +TIPN   +IG+ AF     +</entry></row><row><entry>Sbjct:</entry><entry>264</entry><entry>TIGR-SAFYGCSGLKSITFPNSLTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSGL</entry><entry>322</entry></row><row><entry /></row><row><entry>Query:</entry><entry>251</entry><entry>AEVNLPESLETISDYAFAHMS-LKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAE</entry><entry>309</entry></row><row><entry /><entry /><entry>  + LP+ L TI + AF +   L  + +P+++  IGE AF+       + LP  L  +</entry></row><row><entry>Sbjct:</entry><entry>323</entry><entry>KSITLPDGLTTIEERAFYNCGVLTSITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEW</entry><entry>382</entry></row><row><entry /></row><row><entry>Query:</entry><entry>310</entry><entry>RAFKSNRIQTVEFLGSKLKVIGEASFQD-NNLRNVMLP-DGLEKIESEAF-----TGNPG</entry><entry>362</entry></row><row><entry /><entry /><entry> AF +    T   + + +  IGE++F     L++V +  D    I+ + F     +G</entry></row><row><entry>Sbjct:</entry><entry>383</entry><entry>GAFYNCGALTSITIPNSVSTIGESAFYGCGALKDVTVAWDTPIDIQRDVFRELTLSGIRL</entry><entry>442</entry></row><row><entry /></row><row><entry>Query:</entry><entry>363</entry><entry>DEHYNNQVVLRTRTGQNPHQLATEN-------TYVNPDKSLWRATPDMDYTKWLEEDFTY</entry><entry>415</entry></row><row><entry /><entry /><entry>      + V   +       +  ++        Y    K+L    P  D  K +  +F</entry></row><row><entry>Sbjct:</entry><entry>443</entry><entry>HVPAGKKTVYEAKDVWKEFNIVEDDDFGGLQWNYDAATKTLTITNPTPDTPKPM-PNFAT</entry><entry>501</entry></row><row><entry /></row><row><entry>Query:</entry><entry>416</entry><entry>QKNSVTGFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNVDFQSKTLRKYDLEEIK</entry><entry>475</entry></row><row><entry /><entry /><entry>  + + G   K +QK+             G  +T +GD AF   D          L+ I</entry></row><row><entry>Sbjct:</entry><entry>502</entry><entry>PNDQLWGAFQKEIQKIT-----------IGDGVTSVGDFAFSGCD---------ALKSIT</entry><entry>541</entry></row><row><entry /></row><row><entry>Query:</entry><entry>476</entry><entry>LPSTIRKIGAFAFQSN-NLKSFEASEDLEEIKEGAFMN-NRIGTLDLKDKLIKIGDAAFH</entry><entry>533</entry></row><row><entry /><entry /><entry>LP ++  IG  AF    +L+S    + +  I E AF +   + ++ +   +  IG   FH</entry></row><row><entry>Sbjct:</entry><entry>542</entry><entry>LPKSVTTIGQSAFSGCWDLRSLTLPDGVNTIGEKAFYDCLELTSITIPKSVTAIGQETFH</entry><entry>601</entry></row><row><entry /></row><row><entry>Query:</entry><entry>534</entry><entry>-INHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMAF</entry><entry>577</entry></row><row><entry /><entry /><entry>    + ++ LP+++. IG+ AF    AL  +     + TIGE AF</entry></row><row><entry>Sbjct:</entry><entry>602</entry><entry>YCVSLTSLTLPDALTAIGKKAFYSCNALTSVTFPKSITTIGENAF</entry><entry>646</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 98/351 (27%), Positives = 152/351 (42%), Gaps = 53/351 (15%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>315</entry><entry>NRIQTVEFLGSKLKVIGEASFQDNNLRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRT</entry><entry>374</entry><entry /></row><row><entry /><entry /><entry>++IQTV  +G  +  +G  +F D  L +V LP+ L  I   AF G  G         L +</entry></row><row><entry>Sbjct:</entry><entry>68</entry><entry>SKIQTVT-IGDGVTSVGNNAFSDCALTSVTLPNSLTAIGDHAFKGCSG---------LTS</entry><entry>117</entry></row><row><entry /></row><row><entry>Query:</entry><entry>375</entry><entry>RTGQNPHQLATENTYVNPDKSLWRATPDMDYTKWLEEDFTYQKNSVTGFSNKGLQKVRRN</entry><entry>434</entry></row><row><entry /><entry /><entry> T   P+ + T   +     S  ++                  NS+T      L</entry></row><row><entry>Sbjct:</entry><entry>118</entry><entry>IT--IPNSVTTIGEWAFKGCSGLKSIT--------------LPNSLTAIGQSALSGCTGL</entry><entry>161</entry></row><row><entry /></row><row><entry>Query:</entry><entry>435</entry><entry>KNLEIPKQHNGITITEIGDNAF------RNVDFQSKTLRKYD--------LEEIKLPSTI</entry><entry>480</entry></row><row><entry /><entry /><entry> ++ IP      ++T IG+ AF       ++ F +      +        L  I LP  +</entry></row><row><entry>Sbjct:</entry><entry>162</entry><entry>TSITIPN-----SVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGALTSITLPDAL</entry><entry>216</entry></row><row><entry /></row><row><entry>Query:</entry><entry>481</entry><entry>RKIGAFAFQS-NNLKSFEASEDLEEIKEGAFMN-NRIGTLDLKDKLIKIGDAAFH-INHI</entry><entry>537</entry></row><row><entry /><entry /><entry>  IG  AF+  + LKS      L  I E AF +   + ++ L D L  IG +AF+  + +</entry></row><row><entry>Sbjct:</entry><entry>217</entry><entry>TTIGESAFKGCSGLKSITFPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGL</entry><entry>276</entry></row><row><entry /></row><row><entry>Query:</entry><entry>538</entry><entry>YAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMAFLS-NKLESVNLSEQKQLKTI</entry><entry>596</entry></row><row><entry /><entry /><entry> +I  P S+  IG SAF   G+L  + I N V TIG  AF   + L+S+ L +   L TI</entry></row><row><entry>Sbjct:</entry><entry>277</entry><entry>KSITFPNSLTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSGLKSITLPD--GLTTI</entry><entry>334</entry></row><row><entry /></row><row><entry>Query:</entry><entry>597</entry><entry>EVQAFSD-NALSEVVLPPNLQTIREEAFKR-NHLKEVKGSSTLSQITFNAF</entry><entry>645</entry></row><row><entry /><entry /><entry>E +AF +   L+ + +P ++ TI E AF   + LK +     L+ I + AF</entry></row><row><entry>Sbjct:</entry><entry>335</entry><entry>EERAFYNCGVLTSITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAF</entry><entry>385</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 78/282 (27%), Positives = 123/282 (42%), Gaps = 46/282 (16%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>111</entry><entry>NDASKVEVPKQDTASKKETLETSTWEAKDFVTRGDTLVGFSKSGINKLSQTSHLVLPS--</entry><entry>168</entry><entry /></row><row><entry /><entry /><entry>N+AS  E+P     SK +T           VT GD +     +  +  + TS + LP+</entry></row><row><entry>Sbjct:</entry><entry>56</entry><entry>NNAS--EIPWHSLQSKIQT-----------VTIGDGVTSVGNNAFSDCALTS-VTLPNSL</entry><entry>101</entry></row><row><entry /></row><row><entry>Query:</entry><entry>169</entry><entry>-----HAADG----------TQLTQVASFAFT----------PDKKTAIAEYTSRLGENG</entry><entry>203</entry></row><row><entry /><entry /><entry>     HA  G            +T +  +AF           P+  TAI + ++  G  G</entry></row><row><entry>Sbjct:</entry><entry>102</entry><entry>TAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNSLTAIGQ-SALSGCTG</entry><entry>160</entry></row><row><entry /></row><row><entry>Query:</entry><entry>204</entry><entry>KPSRLDIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETIS</entry><entry>263</entry></row><row><entry /><entry /><entry>  S    +    I E   F    LT +T PN   +IG+ AF     +  + LP++L TI</entry></row><row><entry>Sbjct:</entry><entry>161</entry><entry>LTSITIPNSVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGALTSITLPDALTTIG</entry><entry>220</entry></row><row><entry /></row><row><entry>Query:</entry><entry>264</entry><entry>DYAFAHMS-LKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKS-NRIQTVE</entry><entry>321</entry></row><row><entry /><entry /><entry>+ AF   S LK +  P++L  IGE AF+D      + LP  L  +   AF   + ++++</entry></row><row><entry>Sbjct:</entry><entry>221</entry><entry>ESAFKGCSGLKSITFPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGLKSIT</entry><entry>280</entry></row><row><entry /></row><row><entry>Query:</entry><entry>322</entry><entry>FLGSKLKVIGEASFQD-NNLRNVMLPDGLEKIESEAFTGNPG</entry><entry>362</entry></row><row><entry /><entry /><entry>F  S L  IGE++F +  +L ++ +P+ +  I   AF G  G</entry></row><row><entry>Sbjct:</entry><entry>281</entry><entry>FPNS-LTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSG</entry><entry>321</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 43/144 (29%), Positives = 70/144 (47%), Gaps = 4/144 (2%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>220</entry><entry>EIFNAYQ--LTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFAHM-SLKQVK</entry><entry>76</entry><entry /></row><row><entry /><entry /><entry>+++ A+Q  + K+TI +G  S+G  AF     +  + LP+S+ TI   AF+    L+ +</entry></row><row><entry>Sbjct:</entry><entry>505</entry><entry>QLWGAFQKEIQKITIGDGVTSVGDFAFSGCDALKSITLPKSVTTIGQSAFSGCWDLRSLT</entry><entry>564</entry></row><row><entry /></row><row><entry>Query:</entry><entry>277</entry><entry>LPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQ</entry><entry>336</entry></row><row><entry /><entry /><entry>LPD +  IGE AF+D      + +P+ +  + +  F      T   L   L  IG+ +F</entry></row><row><entry>Sbjct:</entry><entry>565</entry><entry>LPDGVNTIGEKAFYDCLELTSITIPKSVTAIGQETFHYCVSLTSLTLPDALTAIGKKAFY</entry><entry>624</entry></row><row><entry /></row><row><entry>Query:</entry><entry>337</entry><entry>D-NNLRNVMLPDGLEKIESEAFTG</entry><entry>359</entry></row><row><entry /><entry /><entry>  N L +V  P  +  I   AF G</entry></row><row><entry>Sbjct:</entry><entry>625</entry><entry>SCNALTSVTFPKSITTIGENAFDG</entry><entry>648</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 43/134 (32%), Positives = 66/134 (49%), Gaps = 12/134 (8%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="center" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>511</entry><entry>MNNRIGTLDLKDKLIKIGDAAFHINHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVK</entry><entry>570</entry><entry /></row><row><entry /><entry /><entry>+ ++I T+ + D +  +G+ AF    + ++ LP S+  IG  AF+    L  + I N V</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>LQSKIQTVTIGDGVTSVGNNAFSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVT</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>571</entry><entry>TIGEMAFLS-NKLESVNLSEQKQLKTIEVQAFSD-NALSEVVLPPNLQTIREEAFKRNHL</entry><entry>628</entry></row><row><entry /><entry /><entry>TIGE AF   + L+S+ L     L  I   A S    L+ + +P ++ TI E AF</entry></row><row><entry>Sbjct:</entry><entry>126</entry><entry>TIGEWAFKGCSGLKSITL--PNSLTAIGQSALSGCTGLTSITIPNSVTTIGEWAF-----</entry><entry>178</entry></row><row><entry /></row><row><entry>Query:</entry><entry>629</entry><entry>KEVKGSSTLSQITF</entry><entry>642</entry></row><row><entry /><entry /><entry>    G S L+ ITF</entry></row><row><entry>Sbjct:</entry><entry>179</entry><entry>---FGCSGLTSITF</entry><entry>189</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 801&gt; which encodes the amino acid sequence &lt;SEQ ID 802&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00777" num="00777"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 21</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have a cleavable N-term signal seq.</entry></row><row><entry /></row><row><entry>INTEGRAL   Likelihood = −2.44   Transmembrane 984-1000 (984-1001)</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial membrane --- Certainty = 0.1977 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>              bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>LPXTG motif: 975-979</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00778" num="00778"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="329pt" align="left" /><colspec colname="2" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Identities = 751/1050 (71%), Positives 861/1050 (81%), Gaps = 45/1050 (4%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="21pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="21pt" align="char" char="." /><colspec colname="5" colwidth="112pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>3</entry><entry>KKHLKTLALALTTVSVVTYSQEVYGLEREESVKQEQTQSA-SEDDWFEEDNERKTNVSKE</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>KKHLKT+AL LTTVSVVT++QEV+ L  +E +K Q Q S+  S  D+ E +   K +++</entry></row><row><entry>Sbjct:</entry><entry>2</entry><entry>KKHLKTVALTLTTVSVVTHNQEVFSLVKEPILKQTQASSSISGADYAESSGKSKLKINET</entry><entry>61</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>NSTVDETVSDLFSDGNSWNSSSKTESVVSDPKQVPKAKPEVTQEASWSSNDASKVEVPKQ</entry><entry>121</entry></row><row><entry /><entry /><entry>+  VD+TV+DLFSD  +     K        +Q  KA  E T E+       S++E  K+</entry></row><row><entry>Sbjct:</entry><entry>62</entry><entry>SGPVDDTVTDLFSDKRTTPEKIKDNLAKGPREQELKAVTENT-ESEKQITSGSQLEQSKE</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>DTASKKETLETSTWEAKDFVTRGDTLVGFSKSGIWKLSQTSHLVLPSHAADGTQLTQVAS</entry><entry>181</entry></row><row><entry /><entry /><entry>   + K    TS WE  DF+T+G+TLVG SKSG+ KLSQT NLVLPS AADGTQL QVAS</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>SLSLNKTVPSTSNWEICDFITKGWTLVGLSKSGVEKLSQTDHLVLPSQAADGTQLIQVAS</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>FAFTPDKKTAIAEYTSRLGENGKPSRLDIDQKEIIDEGEIFWAYQLTKLTIPNGYKSIGQ</entry><entry>241</entry></row><row><entry /><entry /><entry>FAFTPDKKTAIAEYTSR GENG+ S+LD+D KEII+EGE+FN+Y L K+TIP GYK IGQ</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>FAFTPDKKTAIAEYTSRAGENGEISQLDVDGKEIINEGEVFWSYLLKKVTIPTGYKHIGQ</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>DAFVDNKNIAEVNLPESLETISDYAFAHMSLKQVKLPDWLKVIGELAFFDNQIGGKLYLP</entry><entry>301</entry></row><row><entry /><entry /><entry>DAFVDNKNIAEVWLPESLETISDYAFAH++LKQ+ LPDWLK IGELAFFDNQI GKL LP</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>DAFVDNKNIAEVNLPESLETISDYAFAHLALKQIDLPDWLKAIGELAFFDWQITGKLSLP</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>RHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQDWNLRNVMLPDGLEKIESEAFTGNF</entry><entry>361</entry></row><row><entry /><entry /><entry>R L++LAERAFKSN I+T+EF G+ LKVIGEASFQDN+L  +MLPDGLEKIESEAFTGNP</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>RQLMRLAERAFKSNHIKTIEFRGNSLKVIGEASFQDWDLSQLMLPDGLEKIESEAFTGNP</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>362</entry><entry>GDEHYNNQVVLRTRTGQNPHQLATENTYVNPDKSLWRATPDMDYTKWLEEDFTYQKWSVT</entry><entry>421</entry></row><row><entry /><entry /><entry>GD+HYNN+VVL T++G+NP  LATENTYVNPDKSLW+ +P++DYTKWLEEDFTYQKNSVT</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>GDDHYWNRVVLWTKSGKNPSGLATENTYVNPDKSLWQESPEIDYTKWLEEDFTYQKWSVT</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>422</entry><entry>GFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNVDFQSKTLRKYDLEEIKLPSTIR</entry><entry>481</entry></row><row><entry /><entry /><entry>GFSNKGLQKV+RNKNLEIPKQHNG+TITEIGDNAFRNVDFQ+KTLRKYDLEE+KLPSTIR</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>GFSNKGLQKVKRNKNLEIPKQHNGVTITEIGDNAFRNVDFQNKTLRKYDLEEVKLPSTIR</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>482</entry><entry>KIGAFAFQSNNLKSFEASEDLEEIKEGAFMNNRIGTLDLKDKLIKIGDAAFHINHIYAIV</entry><entry>541</entry></row><row><entry /><entry /><entry>KIGAFAFQSNNLKSFEAS+DLEEIKEGAFMNNRI TL+LKDKL+ IGDAAFHINHIYAIV</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>KIGAFAFQSNNLKSFEASDDLEEIKEGAFMNNRIETLELKDKLVTIGDAAFHINHIYAIV</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>542</entry><entry>LPESVQEIGRSAFRQNGALHLMFIGNKVKTIGSMAFLSNKLSSVNLSEQKQLKTIEVQAF</entry><entry>601</entry></row><row><entry /><entry /><entry>LPESVQEIGRSAFRQNGA +L+F+G+KVKT+GEMAFLSN+LE ++LSEQKQL  I VQAF</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>LPESVQEIGRSAFRQNGANNLIFNGSKVKTLGEMAFLSNRLEHLDLSEQKQLTSIPVQAF</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>602</entry><entry>SDNALSEVVLPPNLQTIREEAFKRNHLKEVKGSSTLSQITFNAFDQNDGDKRFGKKVVVR</entry><entry>661</entry></row><row><entry /><entry /><entry>SDNAL EV+LP +L+TIREEAFK+NHLK+++ +S LS I FNA D NDGD++F   KVVV+</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>SDNALKEVLLFASLKTIREEAFKKNHLKQLEVASALSHIAFNALDDNDGDEQFDNKVVVK</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>662</entry><entry>THNNSHMLADGERFIIDPDKLSSTMVDLEKVLKIIEGLDYSTLRQTTQTQFREMTTAGKA</entry><entry>721</entry></row><row><entry /><entry /><entry>TH+NS+ LADGE FI+DPDKLSST+VDLEK+LK+IEGLDYSTLRQTTQTQFR+MTTAGKA</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>THHNSYALADGEHFIVDPDKLSSTIVDLEKILKLIEGLDYSTLRQTTQTQFRDMTTAGKA</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>722</entry><entry>LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNGHLLERSINKAVL</entry><entry>781</entry></row><row><entry /><entry /><entry>LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNG LLERSINKAVL</entry></row><row><entry>Sbjct:</entry><entry>721</entry><entry>LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNGQLLERSINKAVL</entry><entry>780</entry></row><row><entry /></row><row><entry>Query:</entry><entry>782</entry><entry>AYNNSAIKKANVKRLEKELDLLTDLVEGKGPLAQATMVQGVYLLKTPLPLFEYYIGLNVY</entry><entry>841</entry></row><row><entry /><entry /><entry>AYNNSAIKKANVKRLEKELDLLT LVEGKGPLAQATMVQGVYLLKTPLPLPEYYIGLNVY</entry></row><row><entry>Sbjct:</entry><entry>781</entry><entry>AYNNSAIKKANVKRLEKELDLLTGLVEGKGPLAQATMVQGVYLLKTPLPLPEYYIGLNVY</entry><entry>840</entry></row><row><entry /></row><row><entry>Query:</entry><entry>842</entry><entry>FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYHTLAVATLADYEGLYIKDILN</entry><entry>901</entry></row><row><entry /><entry /><entry>FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYH LAVATLADYEGL IK ILN</entry></row><row><entry>Sbjct:</entry><entry>841</entry><entry>FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYHALAVATLADYEGLDIKTILN</entry><entry>900</entry></row><row><entry /></row><row><entry>Query:</entry><entry>902</entry><entry>SSLDKIKAIRQIPLAKYHRLGIFQAIRNAAAEADRLLPKTPKGYLNEVPNYRKKQVEKNL</entry><entry>961</entry></row><row><entry /><entry /><entry>S L ++ +IRQ+P A YHR GIFQAI+NAAAEA++LLPK</entry></row><row><entry>Sbjct:</entry><entry>901</entry><entry>SKLSQLTSIRQVPTAAYHRAGIFQAIQNAAAEAEQLLPK---------------------</entry><entry>939</entry></row><row><entry /></row><row><entry>Query:</entry><entry>962</entry><entry>KPVDYKTPIFNKALPNEKVDGDRAAKGHNINAETNNSVAVTPIRSEQQLHKSQSDVNLPQ</entry><entry>1021</entry></row><row><entry /><entry /><entry>                     ++++   + N++         ++S  + ++ +    LP+</entry></row><row><entry>Sbjct:</entry><entry>940</entry><entry>----------------PGTHSEKSSSSESANSKDRG------LQSNPKTNRGRHSAILPR</entry><entry>977</entry></row><row><entry /></row><row><entry>Query:</entry><entry>1022</entry><entry>TSSKNNFIYEILGYVSLCLLFLVTAGKKGK</entry><entry>1051</entry></row><row><entry /><entry /><entry>T SK +F+Y ILGY S+ LL L+TA KK K</entry></row><row><entry>Sbjct:</entry><entry>978</entry><entry>TGSKGSFVYGILGYTSVALLSLITAIKKKK</entry><entry>1007</entry></row></tbody></tgroup></table></tables>

SEQ ID 800 (GBS97) was expressed in <i>E. coli </i>as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in <figref idrefs="DRAWINGS">FIG. 17</figref> (lane 12; MW 113.4 kDa).

GBS97-His was purified as shown in <figref idrefs="DRAWINGS">FIG. 193</figref>, lane 6.

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 254

A DNA sequence (GBSx0269) was identified in <i>S. agalactiae </i>&lt;SEQ ID 803&gt; which encodes the amino acid sequence &lt;SEQ ID 804&gt;. This protein is predicted to be ribonucleoside-diphosphate reductase alpha chain (nrdE). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00779" num="00779"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 48</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.4274 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00780" num="00780"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAB96160 GB:AE000050 ribonucleoside-diphosphate reductase</entry><entry /></row><row><entry>alpha</entry></row><row><entry /></row><row><entry>           chain~MPN324 (new), 513 (Himmelreich et al., 1996)</entry></row><row><entry>           [<i>Mycoplasma pneumoniae</i>]</entry></row><row><entry /></row><row><entry>Identities = 476/725 (65%), Positives = 586/725 (80%),</entry></row><row><entry>Gaps = 20/725 (2%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>TQSD--AYLSLNAKTRFRDRTGNYHFTSDKEAVEQYMIEHVEPNTHVFTSLIEKLDYLVS</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>TQ D  +Y+SLNA T+         F  D  AVE Y+ EHV+P T VF S  E+LD+LV</entry></row><row><entry>Sbjct:</entry><entry>12</entry><entry>TQEDLESYISLNAYTKVYG-----DFKMDLHAVEAYIQEHVKPKTKVFHSTKERLDFLVK</entry><entry>66</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>NNYYESDLLKQYNLEFICQIFEHAYAKKFAFLNFHGALKFYNAYALKTEDNRYYLEHYED</entry><entry>119</entry></row><row><entry /><entry /><entry>N+YY+ +++  Y+ E   +I   AYA +F + NFMGA KFYNAYALKT D ++ YLE+YED</entry></row><row><entry>Sbjct:</entry><entry>67</entry><entry>NDYYDENIINMYSFEQFEEITRRAYAYRFRYANFHGAFKFYNAYALKTFDGKWYLENYED</entry><entry>126</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>RVVMNALFLAAGDEKAAYDLVDDMLANRFQPATPTFLNAGKKRRGEYISCYLLRIEDNME</entry><entry>179</entry></row><row><entry /><entry /><entry>RVVMN LFLA G+   A  L+  ++ NRFQPATPTFLNAG+K+RGE++SCYLLRIEDNME</entry></row><row><entry>Sbjct:</entry><entry>127</entry><entry>RVVMNVLFLANGNYNKALKLLKQIITNRFQPATPTFLNAGRKKRGEFVSCYLLRIEDNME</entry><entry>186</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>SISRAISTSLQLSRRGGGVALCLTNLREFGAFIRGIKNQATGIVPVNKLLEDSFSYANQL</entry><entry>239</entry></row><row><entry /><entry /><entry>SI RAI+T+LQLSKR GGVAL LTN+RE GAPIK I+NQ++GI+P+MKLLEDSFSYANQL</entry></row><row><entry>Sbjct:</entry><entry>187</entry><entry>SIGRAITTTLQLSRRDGGVALLLTNIRESGAPIRRIENQSSGIIPIMRLLEDSFSYANQL</entry><entry>246</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>GQRQGAGAVYLHAHHPEVLTFLDTRRENADEKIRIKSLSLGLVIPDITFELAKANKDMAL</entry><entry>299</entry></row><row><entry /><entry /><entry>GQRQGAGAVYLHAHHP+V+ FLDTKRENADEEIRIRSLSLGLVIPDITF LAK N++MAL</entry></row><row><entry>Sbjct:</entry><entry>247</entry><entry>GQRQGAGAVYLHAHHPDVMQFLDTKRENADEKIRIKSLSLGLVIPDITFTLAKNNEEMAL</entry><entry>306</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>FSPYDIERVYGKPMSDISITEEYETLLANADIRKTFISARKLFQTIAELHFESGYPYILF</entry><entry>359</entry></row><row><entry /><entry /><entry>FSPYD+   YGKP+SDIS+TE Y  LLAN  I+KTFI+ARK FQT+AELHFESGYPYILF</entry></row><row><entry>Sbjct:</entry><entry>307</entry><entry>FSPYDVYEEYGKPLSDISVTEMYYELLANQRIKKTFINARKFFQTVAELHFESGYPYILF</entry><entry>366</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>EDTVNAKNPHKKEGRIVMSNLCSEIAQVNTASQFSEDLTFTKVGHDVCCNLGSINIARAM</entry><entry>419</entry></row><row><entry /><entry /><entry>+DTVN +N H    RIVMSNLCSEI Q +T S+F  DL F KVG+D+ CNLGS+NIA+AM</entry></row><row><entry>Sbjct:</entry><entry>367</entry><entry>DDTVNRRNAH--PNRIVMSNLCSEIVQPSTPSEFHHDLAFKKVGNDISCNLGSLNIARAM</entry><entry>424</entry></row><row><entry /></row><row><entry>Query:</entry><entry>420</entry><entry>DQAADFEKLIANSIRALDRVSRTSDLDSAPSIKKGNAANHAVGLGANNLHGFLATNHIYY</entry><entry>479</entry></row><row><entry /><entry /><entry>+   +F +L+  +I +LD VSR S+L++APSI+KGN+  NHA+GLGAMNLHGFLATH IYY</entry></row><row><entry>Sbjct:</entry><entry>425</entry><entry>ESGPEFSELVKLAIESLDLVSRVSNLETAPSIQKGNSENHALGLGANNLHGFLATNQIYY</entry><entry>484</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>DSQEAIDFTDCFFYANAYYAFKASNHLAKEKGTFEGFSESSYADGSYFYQY--TEQNF-E</entry><entry>536</entry></row><row><entry /><entry /><entry>+S EAIDFT+ FFY +AY+AFKAS+ LA ERG F+ F  + +ADGSYF +Y   E +F</entry></row><row><entry>Sbjct:</entry><entry>485</entry><entry>NSFEAIDFTNIFFYTVAYHAFKASSELALEKGKFKNFENTKFADGSYFDKYIKVEPDFWT</entry><entry>544</entry></row><row><entry /></row><row><entry>Query:</entry><entry>537</entry><entry>PKTQRVKNLLAEYGLTLPSQEDWRKLVQSIKEIGLANAHLLAVAPTGSISYLSSCTPSLQ</entry><entry>596</entry></row><row><entry /><entry /><entry>PKT+RVK L  +Y + +P++E+W++L  +I++  GLAN+HLLA+APTGSISYLSSCTPSLQ</entry></row><row><entry>Sbjct:</entry><entry>545</entry><entry>PKTERVKALFQKYQVEIPTRENWKELALNIQKNGLANSHLLAIAPTGSISYLSSCTPSLQ</entry><entry>604</entry></row><row><entry /></row><row><entry>Query:</entry><entry>597</entry><entry>PVVSPVEVRKEGALGRVYVPAYKIDADNYVYYKKGAYEVGSEAIINIAAAAQKHIDQAIS</entry><entry>656</entry></row><row><entry /><entry /><entry>PVVSPVEVRKEG LGR+YVPAY+++ D+Y +YK GAYE+G E IINIAAAAQ+H+DQAIS</entry></row><row><entry>Sbjct:</entry><entry>605</entry><entry>PVVSPVEVRKEGRLGRIYVPAYQLNEDSYPFYKDGAYELGPEPIINIAAAAQQHVDQAIS</entry><entry>664</entry></row><row><entry /></row><row><entry>Query:</entry><entry>657</entry><entry>LTLFMTDQATTRDLNKAYIQAFKQKCASIYYVRVRQDILEGSESYDDMLDDFTSSDLEDC</entry><entry>716</entry></row><row><entry /><entry /><entry>LTLFMTD+ATTRDLNKAYI AFK+ C+SIYYVRVRQ++LE SE +        +  ++ C</entry></row><row><entry>Sbjct:</entry><entry>665</entry><entry>LTLFMTDKATTRDLNKAYIYAFKKGCSSIYYVRVRQEVLEDSEDH--------TIQMQQC</entry><entry>716</entry></row><row><entry /></row><row><entry>Query:</entry><entry>717</entry><entry>QSCMI</entry><entry>721</entry></row><row><entry /><entry /><entry>++C+I</entry></row><row><entry>Sbjct:</entry><entry>717</entry><entry>EACVI</entry><entry>721</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 805&gt; which encodes the amino acid sequence &lt;SEQ ID 806&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00781" num="00781"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="343pt" align="left" /><colspec colname="2" colwidth="98pt" align="left" /><tbody valign="top"><row><entry>Possible site: 47</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>               bacterial cytoplasm --- Certainty = 0.1843 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                 bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the databases:

<tables id="TABLE-US-00782" num="00782"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC82625 GB:AF054892 surface antigen BspA [<i>Bacteroides forsythus</i>]</entry><entry /></row><row><entry /></row><row><entry>Identities = 124/451 (27%), Positives = 202/451 (44%),</entry></row><row><entry>Gaps = 65/451 (14%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>221</entry><entry>FNSYLLKKVTIPTGYKHIGQDAFVDNKNIAEVNLPSSLETISDYAFAHLA-LKQIDLPDN</entry><entry>279</entry><entry /></row><row><entry /><entry /><entry>F+   L  VT+P     IG  AF     +  + +P S+ TI ++AF   + LK I LP++</entry></row><row><entry>Sbjct:</entry><entry>87</entry><entry>FSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNS</entry><entry>146</entry></row><row><entry /></row><row><entry>Query:</entry><entry>280</entry><entry>LKAIGELAFFDNQITGKLSLPRQLMRLAERA-FKSNHIKTISFRGNSLKVIGEASFQD-N</entry><entry>337</entry></row><row><entry /><entry /><entry>L AIG+A         +++P  +  + E A F  + +  +I F  NSL  IGE++F</entry></row><row><entry>Sbjct:</entry><entry>147</entry><entry>LTAIGQSALSGCTGLTSITIPNSVTTIGEWAFFGCSGLTSITF-PNSLTAIGESAFYGCG</entry><entry>205</entry></row><row><entry /></row><row><entry>Query:</entry><entry>338</entry><entry>DLSQLMLPDGLEKIESEAFTGNPGDDHYNNRVVLWTKSGKNPSGLATENTYVNPDKSLWQ</entry><entry>397</entry></row><row><entry /><entry /><entry> L+ + LPD L  I   AF G  G            KS   P+ L T        +S +</entry></row><row><entry>Sbjct:</entry><entry>206</entry><entry>ALTSITLPDALTTIGESAFKGCSG-----------LKSITFPNSLTTIG------ESAFY</entry><entry>248</entry></row><row><entry /></row><row><entry>Query:</entry><entry>398</entry><entry>SSPEIDYTKWLEEDFTYQKNSVTGFSNKGLQKVKRNKNLSIPKQHNGVTITEIGDNAFRN</entry><entry>457</entry></row><row><entry /><entry /><entry>+   +      +   T  +++  G S  GL      K++  P       ++T IG++AF N</entry></row><row><entry>Sbjct:</entry><entry>249</entry><entry>DCGALTSITLPDALTTIGRSAFYGCS--GL------KSITFPN-----SLTTIGESAFYN</entry><entry>295</entry></row><row><entry /></row><row><entry>Query:</entry><entry>458</entry><entry>VDFQNKTLRKYDLEEVKLPSTIRKIGAFAFQS-NNLKSFEASDDLEEIKEGAFMNNRIET</entry><entry>516</entry></row><row><entry /><entry /><entry>            L  + +P+++  IG  AF   + LKS    D L  I+E AF N  + T</entry></row><row><entry>Sbjct:</entry><entry>296</entry><entry>CG---------SLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLT</entry><entry>346</entry></row><row><entry /></row><row><entry>Query:</entry><entry>517</entry><entry>-LELKDKLVTIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGANNLIFNGSKVKTLGEM</entry><entry>574</entry></row><row><entry /><entry /><entry> + + + + TIG++AF+  + + +I  LP+ +  I   AF   GA   I + + V T+GE</entry></row><row><entry>Sbjct:</entry><entry>347</entry><entry>SITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAFYNCGALTSITIPNSVSTIGES</entry><entry>406</entry></row><row><entry /></row><row><entry>Query:</entry><entry>575</entry><entry>AFLS-NRLEHLDLSEQKQLTEIPVQAFSDNALKEVLL--PASLKTIREEAFKKNHLKQLE</entry><entry>631</entry></row><row><entry /><entry /><entry>AF     L+ + ++    + +I    F +  L  + L  PA  KT+ E    K+   K+</entry></row><row><entry>Sbjct:</entry><entry>407</entry><entry>AFYGCGALKDVTVAWDTPI-DIQRDVFRELTLSGIRLHVPAGKKTVYE---AKDVWKE--</entry><entry>460</entry></row><row><entry /></row><row><entry>Query:</entry><entry>632</entry><entry>VASALSHIAFNALDDND-GDEQFDNKVVVRT</entry><entry>661</entry></row><row><entry /><entry /><entry>         FN ++D+D G  Q++</entry><entry>KT</entry></row><row><entry>Sbjct:</entry><entry>461</entry><entry>---------FNIVEDDDFGGLQWNYDAATKT</entry><entry>482</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00783" num="00783"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 534/726 (73%), Positives = 614/726 (84%),</entry><entry /></row><row><entry /></row><row><entry>Gaps = 5/726 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>1</entry><entry>HTQSDA-YLSLNAKTRFRDRTGNYHFTSDKSAVEQYHIEHVEPNTMVFTSLIEKLDYLVS</entry><entry>59</entry><entry /></row><row><entry /><entry /><entry>M+Q++A YLSLNA TRF+   G+YHF SDKEAV +Y+ EHV PN M F SL +KL YL++</entry></row><row><entry>Sbjct:</entry><entry>1</entry><entry>MSQTNASYLSLNALTRFKKPDGSYHFDSDKEAVRRYLEEHVSPNQMAFNSLEDKLAYLIN</entry><entry>60</entry></row><row><entry /></row><row><entry>Query:</entry><entry>60</entry><entry>NNYYESDLLKQYNLEFICQIFEHAYAKKFAFLNFMGALKFYNAYALKTEDNRYYLEHYED</entry><entry>119</entry></row><row><entry /><entry /><entry>  YYE  +   Y  + I + F +AY + + FLN MGA+KFY +YALKT D +  YLE +ED</entry></row><row><entry>Sbjct:</entry><entry>61</entry><entry>EGYYEQAIFDAYPNDLIKEAFHYAYQQGYRFLNLNGAMKFYQSYALKTLDGKQYLETFED</entry><entry>120</entry></row><row><entry /></row><row><entry>Query:</entry><entry>120</entry><entry>RVVMNALFLAAGDEKAAYDLVDDMLANRFQPATPTFLNAGKERRGEYISCYLLRIEDNME</entry><entry>179</entry></row><row><entry /><entry /><entry>R VMNALFLA GD+   +D++D +L  RFQPATPTFLNAGKKRRGEYISCYLLR+EDNME</entry></row><row><entry>Sbjct:</entry><entry>121</entry><entry>PAVMNALFLADGDQTFVFDVIDAILHRRFQPATPTFLNAGKKRRGEYISCYLLRVEDNME</entry><entry>180</entry></row><row><entry /></row><row><entry>Query:</entry><entry>180</entry><entry>SISRAISTSLQLSKRGGGVALCLTNLREFGAPIKGIKNQATGIVPVMKLLEDSFSYANQL</entry><entry>239</entry></row><row><entry /><entry /><entry>SISRAISTSLQLSKRGGGVALCLTNLRE GAPIKGI+NQATGIVPVMKLLEDSFSYANQL</entry></row><row><entry>Sbjct:</entry><entry>181</entry><entry>SISRAISTSLQLSKRGGGVALCLTNLREIGAPIKGIENQATGIVPVMKLLEDSFSYANQL</entry><entry>240</entry></row><row><entry /></row><row><entry>Query:</entry><entry>240</entry><entry>GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSLSLGLVIPDITFELAKANKDMAL</entry><entry>299</entry></row><row><entry /><entry /><entry>GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSL+LGLVIPDITF+LAK NKDMAL</entry></row><row><entry>Sbjct:</entry><entry>241</entry><entry>GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSLALGLVIPDITFQLAKENKDMAL</entry><entry>300</entry></row><row><entry /></row><row><entry>Query:</entry><entry>300</entry><entry>FSPYDIERVYGKPMSDISITEEYETLLANADIRKTFISARKLFQTIAELHFESGYPYILF</entry><entry>359</entry></row><row><entry /><entry /><entry>FSPYDI+R Y K MSDISITEEY+ LLAN  I+KT+ISARK FQ IAELHFESGYPY+LF</entry></row><row><entry>Sbjct:</entry><entry>301</entry><entry>FSPYDIKRAYGKDMSDISITEEYDKLLANPAIKKTYISARKFFQLIAELHFSSGYPYLLF</entry><entry>360</entry></row><row><entry /></row><row><entry>Query:</entry><entry>360</entry><entry>EDTVNAKNPHKKEGRIVIASNLCSEIAQVNTASQFSEDLTFTKVGHDVCCNLGSINIARM</entry><entry>419</entry></row><row><entry /><entry /><entry>+DTVN +NPH K+GRIVMSNLCSEIAQV+T S F EDL+F +G D+CCNLGSINIA+AN</entry></row><row><entry>Sbjct:</entry><entry>361</entry><entry>DDTVNKRNPHAKKGRIVMSNLCSEIAQVSTPSTFKEDLSFETIGEDICCNLGSINIAQAN</entry><entry>420</entry></row><row><entry /></row><row><entry>Query:</entry><entry>420</entry><entry>DQAADFEKLIANSIRALDRVSRTS0LDSAPSIKKGNAANHAVGLGAMNLHGFLATNNIYY</entry><entry>479</entry></row><row><entry /><entry /><entry>  A  FE+LI  SIRALDRVSR SDL+ APS++ GNAANHAVGLGAMNLHGFLATNHIYY</entry></row><row><entry>Sbjct:</entry><entry>421</entry><entry>ADAPHFEQLITTSIRALDRVSRVSDLNCAPSVETGNAANHAVGLGAMNLHGFLATNNIYY</entry><entry>480</entry></row><row><entry /></row><row><entry>Query:</entry><entry>480</entry><entry>DSQEAIDFTDCFFYAMAYYAFKASNHLAKEKGTFEGFSESSYADGSYFYQYTEQNFEPKT</entry><entry>539</entry></row><row><entry /><entry /><entry>D++EA+DFTD FF+AMAYYAFKAS  LAKEKG F GFS S+Y+DG+YF +Y +++  +P+T</entry></row><row><entry>Sbjct:</entry><entry>481</entry><entry>DTKEAVDFTDLFFHAMAYYAFKASCQLAKEKGAFAGFSLSTYSDGTYFAKYLQEDAKPQT</entry><entry>540</entry></row><row><entry /></row><row><entry>Query:</entry><entry>540</entry><entry>QRVKNLLAEYGLTLPSQEDWRKLVQSIKEIGLANAHLLAVAPTGSISYLSSCTPSLQPVV</entry><entry>599</entry></row><row><entry /><entry /><entry> +V  LL +YG TLP+  DW+ LV  IK+ GLANAHLLAVAPTGSISYLSSCTPSLQPVV</entry></row><row><entry>Sbjct:</entry><entry>541</entry><entry>AKVATLLQDYGFTLPTVADWQALVADIKQFGLANAHLLAVAPTGSISYLSSCTPSLQPVV</entry><entry>600</entry></row><row><entry /></row><row><entry>Query:</entry><entry>600</entry><entry>SPVEVRKEGALGRVYVPAYKIDADNYVYYKRGAYEVGSEAIINIAAAAQKHIDQAISLTL</entry><entry>659</entry></row><row><entry /><entry /><entry>+PVEVRKEG+LGR+YVPAY+ID  NY YY++GAYEVG +AII++ AAAQKH+DQAISLTL</entry></row><row><entry>Sbjct:</entry><entry>601</entry><entry>APVEVRKEGSLGRIYVPAYQIDQANYAYYERGAYEVGPKAIIDVVAAAQKHVDQAISLTL</entry><entry>660</entry></row><row><entry /></row><row><entry>Query:</entry><entry>660</entry><entry>FMTDQATTRDLNKAYIQAFKQKCASIYYVRVRQDILEGSESYDD----MLDDFTSSDLED</entry><entry>715</entry></row><row><entry /><entry /><entry>FMTDQATTRDLN++YIQAFKQ CASIYYVRVRQD+L GSE YD+         +     +</entry></row><row><entry>Sbjct:</entry><entry>661</entry><entry>FMTDQATTRDLNRSYIQAFKQNCASIYYVRVRQDVLAGSEQYDEDSLVTAPGASDETTTE</entry><entry>720</entry></row><row><entry /></row><row><entry>Query:</entry><entry>716</entry><entry>CQSCMI</entry><entry>721</entry></row><row><entry /><entry /><entry>CQSCMI</entry></row><row><entry>Sbjct:</entry><entry>721</entry><entry>CQSCMI</entry><entry>726</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 255

A DNA sequence (GBSx0270) was identified in <i>S. agalactiae </i>&lt;SEQ ID 807&gt; which encodes the amino acid sequence &lt;SEQ ID 808&gt;. This protein is predicted to be nrdI protein (nrdI). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00784" num="00784"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results ----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.2952 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00785" num="00785"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAC71451 GB:U39702 nrdI protein (nrdI) [<i>Mycoplasma genitalium</i>]</entry><entry /></row><row><entry>Identities = 77/127 (60%), Positives = 104/127 (81%), Gaps = 1/127 (0%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="right" /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="right" /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>VVYFSSKSNNTHRFVQKLACSNQRIPSD-GSSILVTEDYILIVPTYAGGGDDTKGAVPKQ</entry><entry>65</entry><entry /></row><row><entry /><entry /><entry>+VYFSS SNNTHRF++KL   ++RIP D   SI V+ +Y+LI PTY+GGG+  +GAVPKQ</entry></row><row><entry>Sbjct:</entry><entry>22</entry><entry>IVYFSSISNNTHRFIEKLGFQHKRIPVDITQSITVSNEYVLICPTYSGGGNQVEGAVPKQ</entry><entry>81</entry></row><row><entry /></row><row><entry>Query:</entry><entry>66</entry><entry>VVQFLNVRQNREHCQGVISSGNTNFGDTYAIAGPIIARKLNVPLLHQFELLGTQEDVTRV</entry><entry>125</entry></row><row><entry /><entry /><entry>V+QFLN + NRE C+GVI+SGNTNFGDT+ +AG +I++KLNVPLL+QFELLGT+ DV +</entry></row><row><entry>Sbjct:</entry><entry>82</entry><entry>VIQFLNNKHNRELCRGVIASGNTNFGDTFCLAGTVISKKLNVPLLYQFELLGTKNDVEQT</entry><entry>141</entry></row><row><entry /></row><row><entry>Query:</entry><entry>126</entry><entry>KELLCQF</entry><entry>132</entry></row><row><entry /><entry /><entry>++++  F</entry></row><row><entry>Sbjct:</entry><entry>142</entry><entry>QKIIANF</entry><entry>148</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 809&gt; which encodes the amino acid sequence &lt;SEQ ID 810&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00786" num="00786"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="280pt" align="left" /><colspec colname="2" colwidth="161pt" align="left" /><tbody valign="top"><row><entry>Possible site: 54</entry><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>bacterial cytoplasm --- Certainty = 0.0089 (Affirmative) &lt; succ&gt;</entry></row><row><entry>bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry>bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00787" num="00787"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 84/125 (67%), Positives = 100/125 (79%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>7</entry><entry>VVYFSSKSNNTHRFVQKLACSNQRIPSDGSSILVTEDYILIVPTYAGGGDDTKGAVPKQV</entry><entry>66</entry><entry /></row><row><entry /><entry /><entry>+VYFSSKS NTHRFVQKL    QRIP D   + V+  Y+LIVPTYA GG D KGAV KQV</entry></row><row><entry>Sbjct:</entry><entry>6</entry><entry>IVYFSSKSNNTHRFVQKLGLPAQRIPVDNRPLEVSTHYLLIVPTYAAGGSDAKGAVSKQV</entry><entry>65</entry></row><row><entry /></row><row><entry>Query:</entry><entry>67</entry><entry>VQFLNVRQNREHCQGVISSGNTNFGDTYAIAGPIIARKLNVPLLHQFELLGTQEDVTRVK</entry><entry>126</entry></row><row><entry /><entry /><entry>++FLN   NR+HC+GVISSGNTNFGDT+A+AGPII++KL VPLLHQFELLGT  DV +V+</entry></row><row><entry>Sbjct:</entry><entry>66</entry><entry>IRFLNNPNNRKHCKGVISSGNTNFGDTFALAGPIISQKLQVPLLHQFELLGTATDVKKVQ</entry><entry>125</entry></row><row><entry /></row><row><entry>Query:</entry><entry>127</entry><entry>ELLCQ</entry><entry>131</entry></row><row><entry /><entry /><entry>++</entry></row><row><entry>Sbjct:</entry><entry>126</entry><entry>AIFAR</entry><entry>130</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 256

A DNA sequence (GBSx0271) was identified in <i>S. agalactiae </i>&lt;SEQ ID 811&gt; which encodes the amino acid sequence &lt;SEQ ID 812&gt;. This protein is predicted to be ribonucleoside-diphosphate reductase beta chain (nrdF). Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00788" num="00788"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 27</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3889 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

The protein has homology with the following sequences in the GENPEPT database:

<tables id="TABLE-US-00789" num="00789"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>&gt;GP:AAB96162 GB:AE000050 ribonucleoside-diphosphate reductase beta</entry><entry /></row><row><entry>chain [<i>Mycoplasma pneumoniae</i>]</entry></row><row><entry /></row><row><entry>Identities = 261/335 (77%), Positives = 301/335 (88%)</entry></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>QSYYDRSQSPLDYALSEKAFPMRSVNWNKLNDDKDLEVWNRVTQNFWLPSKIPVSNDLNS</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>+ Y+  S SPL+YA  +    +RSVNWN ++D+KDLEVWNR+TQNFWLPEKIPVSND+ S</entry></row><row><entry>Sbjct:</entry><entry>5</entry><entry>KKYFLESVSPLEYAQKKPQGNLRSVNWNLVDDEKDLEVWNRITQNFWLPEKIPVSNDIPS</entry><entry>64</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>WRTLDADWQQLITRTFTGLTLLDSVQATVGDIAQIKHSQTDHSQVIYANFAFMVAIHARS</entry><entry>121</entry></row><row><entry /><entry /><entry>W+ L  +WQ LIT+TFTGLTLLD++QAT+GDI QI ++ TDHSQVIYANFAFMV +HARS</entry></row><row><entry>Sbjct:</entry><entry>65</entry><entry>WKQLSKEWQDLITKTFTGLTLLDTIQATIGDIKQIDYALTDHEQVIYANFAFMVGVHARS</entry><entry>124</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>YGTIFSTLCTSQQIEEAHEWVVDTESLQARSRILIPFYTGDDPLKSKVAAAMMPGFLLYG</entry><entry>181</entry></row><row><entry /><entry /><entry>YGTIFSTLCTS+QI EAHEWVV TESLQ R++ LIP+YTG DPLKSKVAAA+MPGFLLYG</entry></row><row><entry>Sbjct:</entry><entry>125</entry><entry>YGTIFSTLCTSEQITEAHEWVVKTESLQKRAKALIPYYTGKDPLKSKVAAALMPGFLLYG</entry><entry>184</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>GFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVAKLSVEKQAEMKTFVFD</entry><entry>241</entry></row><row><entry /><entry /><entry>GFYLPFYLS+R +LPNTSDIIRLILRDKVIHNYYSGYK+Q+KV K+S EKQAEMK FVFD</entry></row><row><entry>Sbjct:</entry><entry>185</entry><entry>GFYLPFYLSSRKQLPNTSDIIRLILRDKVIHNYYSGYKFQRKVEKMSKEKQAEMKRFVFD</entry><entry>244</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>LLYQLIDLEKAYLYELYDGEDLAEDAIRFSIYNAGKFLQNLGYDSPFTEEETRISPEVFA</entry><entry>301</entry></row><row><entry /><entry /><entry>L+Y+LI+LEKAYL ELY+GF + EDAI+FSIYNAGKFLQNLGYDSPFTEESTRI PE+FA</entry></row><row><entry>Sbjct:</entry><entry>245</entry><entry>LMYELIELEKAYLKELYEGEGIVEDAIKFSIYNAGKFLQNLGYDSPFTSEETRIKPEIFA</entry><entry>304</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>QLSARADENHDFFSGMGSSYIMGITEETLDEDWEF</entry><entry>336</entry></row><row><entry /><entry /><entry>QLSARADENHDFFSGNGSSY+MGI+EET D+DW+F</entry></row><row><entry>Sbjct:</entry><entry>305</entry><entry>QLSARADENHDFFSGNGSSYVMGISEETEDKDWDF</entry><entry>339</entry></row></tbody></tgroup></table></tables>

A related DNA sequence was identified in <i>S. pyogenes </i>&lt;SEQ ID 813&gt; which encodes the amino acid sequence &lt;SEQ ID 814&gt;. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00790" num="00790"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 18</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.3779 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>

An alignment of the GAS and GBS proteins is shown below:

<tables id="TABLE-US-00791" num="00791"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="315pt" align="left" /><colspec colname="2" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Identities = 292/335 (87%), Positives = 318/335 (94%)</entry><entry /></row><row><entry /></row></tbody></tgroup><tgroup align="left" colsep="0" rowsep="0" cols="5"><colspec colname="1" colwidth="28pt" align="left" /><colspec colname="2" colwidth="14pt" align="char" char="." /><colspec colname="3" colwidth="259pt" align="left" /><colspec colname="4" colwidth="14pt" align="char" char="." /><colspec colname="5" colwidth="126pt" align="left" /><tbody valign="top"><row><entry>Query:</entry><entry>2</entry><entry>QSYYDRSQSPLDYALSEKAFPMRSVNWNKLNDDKDLEVWNRVTQNFWLPEKIPVSNDLNS</entry><entry>61</entry><entry /></row><row><entry /><entry /><entry>Q YY+RSQSP++YALSE    +RS+NWN LNDDKDLEVWNRVTQNFWLPEK+PVSNDLNS</entry></row><row><entry>Sbjct:</entry><entry>3</entry><entry>QHYYERSQSPIEYALSETQKQLRSINWNYLNDDKDLEVWNRVTQNFWLPEKVPVSNDLNS</entry><entry>62</entry></row><row><entry /></row><row><entry>Query:</entry><entry>62</entry><entry>WRTLDADWQQLITRTFTGLTLLDSVQATVGDIAQIKHSQTDHEQVIYANFAFMVAIHARS</entry><entry>121</entry></row><row><entry /><entry /><entry>WR+L  DWQQLITRT+TGLTLLD+VQATVGD+AQI+HSQTDHEQVIY NFAFMV IHARS</entry></row><row><entry>Sbjct:</entry><entry>63</entry><entry>WRSLGEDWQQLITRTYTGLTLLDTVQATVGDVAQIQHSQTDHEQVIYTNFAFMVGIHARS</entry><entry>122</entry></row><row><entry /></row><row><entry>Query:</entry><entry>122</entry><entry>YGTIFSTLCTSQQIEEAHEWVVDTESLQARSRILIPFYTGDDPLKSKVAAAMMPGFLLYG</entry><entry>181</entry></row><row><entry /><entry /><entry>YGTIFSTLC+S+QIEEAHEWVV T+SLQ R+R+LIP+YTGDDPLKSKVAAAMMPGFLLYG</entry></row><row><entry>Sbjct:</entry><entry>123</entry><entry>YGTIFSTLCSSEQIEEAHEWVVSTQSLQDRARVLIPYYTGDDPLKSKVAAAMMPGFLLYG</entry><entry>182</entry></row><row><entry /></row><row><entry>Query:</entry><entry>182</entry><entry>GFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVAKLSVEKQAEMKTFVFD</entry><entry>241</entry></row><row><entry /><entry /><entry>GFYLPFYLSARGK+PNTSDIIRLILRDKVIHNYYSGYKYQQKVA+LS EKQAEMK FVFD</entry></row><row><entry>Sbjct:</entry><entry>183</entry><entry>GFYLPFYLSARGKMPNTSDIIRLILRDKVIHNYYSGYKYQQKVARLSPEEQAEMKAFVFD</entry><entry>242</entry></row><row><entry /></row><row><entry>Query:</entry><entry>242</entry><entry>LLYQLIDLEKAYLYELYDGFDLAEDAIRWSIYNAGKFLQNLGYDSPFTEEETRISPEVFA</entry><entry>301</entry></row><row><entry /><entry /><entry>LLY+LIDLEKAYL ELY GFDLAEDAIRFS+YNAGKFLQNLGY+SPFT+EETR+SPEVFA</entry></row><row><entry>Sbjct:</entry><entry>243</entry><entry>LLYELIDLEKAYLRELYAGFDLAEDAIRFSLYNAGKFLQNLGYESPFTDEETRVSPEVFA</entry><entry>302</entry></row><row><entry /></row><row><entry>Query:</entry><entry>302</entry><entry>QLSARADENHDFFSGNGSSYIMGITEETLDEDWEF</entry><entry>336</entry></row><row><entry /><entry /><entry>QLSARADENHDFFSGNGSSY+MGITEET D+DWEF</entry></row><row><entry>Sbjct:</entry><entry>303</entry><entry>QLSARADENHDFFSGNGSSYVHGITEETTDDDWEF</entry><entry>337</entry></row></tbody></tgroup></table></tables>

Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics.

EXAMPLE 257

A DNA sequence (GBSx0272) was identified in <i>S. agalactiae </i>&lt;SEQ ID 815&gt; which encodes the amino acid sequence &lt;SEQ ID 816&gt;. This protein is predicted to be rhamnosyltransferase. Analysis of this protein sequence reveals the following:

<tables id="TABLE-US-00792" num="00792"><table frame="none" colsep="0" rowsep="0" pgwide="1" tabstyle="monospace"><tgroup align="left" colsep="0" rowsep="0" cols="2"><colspec colname="1" colwidth="336pt" align="left" /><colspec colname="2" colwidth="105pt" align="left" /><tbody valign="top"><row><entry>Possible site: 55</entry><entry /></row><row><entry /></row><row><entry>&gt;&gt;&gt; Seems to have no N-terminal signal sequence</entry></row><row><entry /></row><row><entry>----- Final Results -----</entry></row><row><entry>              bacterial cytoplasm --- Certainty = 0.1741 (Affirmative) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>               bacterial membrane --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row><row><entry /></row><row><entry>                bacterial outside --- Certainty = 0.0000 (Not Clear) &lt; succ&gt;</entry></row></tbody></tgroup></table></tables>